Abcam Protocols Book 2010

Protocols book
(first edition)
www.abcam.com
Contents
Welcome to Abcam
About Abcam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 Benefits of an Abcam account . . . . . . . . . . . . . . . . . . . . . . . .2 Abreviews and Abpoints . . . . . . . . . . . . . . . . . . . . . . . . . . .2
Protocols
SECTION 1: Antibodies and antibody structure . . . . . . .3
Catalogue contents
SECTION 2: Various formats of antibody and . . . . . . . . .6 antibody purification SECTION 3: Choosing an antibody and antibody dilution . . .7 SECTION 4: Fluorescence . . . . . . . . . . . . . . . . . . . . . . . . .9 4.1 How single fluorochromes work . . . . . . . . . . . . . . . . . . .9 4.2 How tandem dyes work . . . . . . . . . . . . . . . . . . . . . . . . . .9 4.3 Fluorochrome table (excitation and emission wavelengths) . . .11 SECTION 5: Western blot . . . . . . . . . . . . . . . . . . . . . . . .13 5.1 Sample preparation . . . . . . . . . . . . . . . . . . . . . . . . . . .15 Lysis buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15 Protease and phosphatase inhibitors . . . . . . . . . . . . . . .16 Preparation of lysate from cell culture . . . . . . . . . . . . . . .16 Preparation of lysate from tissues . . . . . . . . . . . . . . . . . .16 Determination of protein concentration . . . . . . . . . . . . . .17 Preparation of samples for loading into gels . . . . . . . . . .17 5.2 Electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18 Preparation of PAGE gels . . . . . . . . . . . . . . . . . . . . . . . .18 Positive controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19 Molecular weight markers . . . . . . . . . . . . . . . . . . . . . . . .19 Loading samples and running the gel . . . . . . . . . . . . . . .19 Use of loading controls . . . . . . . . . . . . . . . . . . . . . . . . . .20 5.3 Transfer of proteins and staining . . . . . . . . . . . . . . .20 Visualization of proteins in gels . . . . . . . . . . . . . . . . . . . .20 Transfer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20 Visualization of proteins in membranes: Ponceau Red . . . . .22 Blocking the membrane . . . . . . . . . . . . . . . . . . . . . . . . . .22 Incubation with the primary antibody . . . . . . . . . . . . . . . .22 Incubation with the secondary antibody . . . . . . . . . . . . .22 Development methods . . . . . . . . . . . . . . . . . . . . . . . . . . .23 5.4 Western blot references . . . . . . . . . . . . . . . . . . . . . . .23 5.5 Troubleshooting tips Western blotting . . . . . . . . .24 SECTION 6: Immunohistochemistry . . . . . . . . . . . . . . . .27 6.1 IHC-Paraffin embedded . . . . . . . . . . . . . . . . . . . . . . . . .27 6.1.1 Optimizing a new antibody for IHC-P . . . . . . . . . .29 6.1.2 Deparaffinization . . . . . . . . . . . . . . . . . . . . . . . . . .29
6.1.3 Antigen retrieval . . . . . . . . . . . . . . . . . . . . . . . . . . .30 6.1.4 Immunostaining and detection protocol . . . . . . . . .33 6.1.5 Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37 6.2 IHC-Frozen sections (IHC-Fr) . . . . . . . . . . . . . . . . . . . .37 6.3 Immunocytochemistry (ICC) . . . . . . . . . . . . . . . . . . . . .37 6.4 IHC and ICC fixation and permeabilization tips . . . . . .38 6.5 Perfusion fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40 6.6 Mouse on mouse staining tips . . . . . . . . . . . . . . . . . . . .41 6.7 Troubleshooting tips IHC and ICC . . . . . . . . . . . . . . .42 SECTION 7: ELISA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44 7.1 Indirect ELISA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44 7.2 Direct ELISA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46 7.3 Sandwich ELISA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48 7.4 Troubleshooting tips - ELISA . . . . . . . . . . . . . . . . . . . . .50 SECTION 8: Flow Cytometry (introduction) . . . . . . . . . .53 8.1 Recommended controls for flow cytometry/FACs . . . .55 8.2 Direct Flow cytometry . . . . . . . . . . . . . . . . . . . . . . . . . .56 8.3 Indirect Flow cytometry . . . . . . . . . . . . . . . . . . . . . . . . .57 8.4 Intracellular flow cytometry . . . . . . . . . . . . . . . . . . . . . .58 8.5 Flow cytometry troubleshooting . . . . . . . . . . . . . . . . . .61 SECTION 9: Immunoprecipitation . . . . . . . . . . . . . . . . . .63 9.1 Lysis buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63 9.2 Crosslinking antibody to the beads . . . . . . . . . . . . . . .67 9.3 Using IgM antibodies for IP . . . . . . . . . . . . . . . . . . . . .68 9.4 Troubleshooting tips - IP . . . . . . . . . . . . . . . . . . . . . . .69 SECTION 10: ChIP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71 10.1 X-ChIP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71 10.2 Troubleshooting tips - ChIP . . . . . . . . . . . . . . . . . . . .76 SECTION 11: Buffers and stock solutions . . . . . . . . . . .77 11.1 Standard PBS, TBS, TBS Tween . . . . . . . . . . . . . . . .77 11.2 Western blot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77 11.3 IHC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79 11.4 ELISA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80 11.5 Flow Cytometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80 11.6 IP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80 11.7 ChIP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80 SECTION 12: Antibody storage guide . . . . . . . . . . . . . .82
Technical help
Online resources at Abcam . . . . . . . . . . . . . . . . . . . . . . . . .84 Product datasheet guide . . . . . . . . . . . . . . . . . . . . . . . . . . .84 Online protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85 Online poster library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Ordering and contact details

Contact details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86 Local offices and distributors . . . . . . . . . . . . . . . . . . . . . . . .87 Required information for ordering . . . . . . . . . . . . . . . . . . . .88 Abcams terms and conditions . . . . . . . . . . . . . . . . . . . . . .89
View complete catalog and ordering information: www.abcam.com Scientific support: www.abcam.com/technical
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SECTION 1: Antibodies and antibody structure

Antibodies, also called immunoglobulins (Ig), are glycoproteins that are capable of specifically binding to antigens that caused their production in a susceptible animal. They are produced in response to the invasion of foreign molecules in the body. Antibodies exist as one or more copies of a Y-shaped unit, composed of four polypeptide chains. Each Y contains two copies of a heavy chain, and two copies of a light chain, named as such by their relative molecular weights. The top of the Y shape contains the variable region, which is the antigen binding site. The light chains of any antibody can be classified as either a kappa () or lambda () type (based on small polypeptide structural differences); however, the heavy chain determines the class, or isotype, of each antibody.
Antibody structure:
light chain N
VL
or N N
N
VH
VH VL
Fab (Fab)2
CH 1
antigen binding
CL
SS
CHO
CH2
biological activity
C CH2 CH3 C
S S S S
C
CHO
CL
Heavy chains
There are five types of mammalian Ig heavy chains denoted by the Greek letters: alpha (), delta (), epsilon (), gamma (), and mu (). These chains are found in IgA, IgD, IgE, IgG, and IgM antibodies, respectively. Distinct heavy chains differ in size and composition; and contain approximately 450 amino acids, while and have approximately 550 amino acids. Each heavy chain has two regions, the constant region and the variable region. The constant region is identical in all antibodies of the same isotype, but differs in antibodies of different isotypes. Heavy chains , and have a constant region composed of three tandem (in a line) Ig domains, and a hinge region for added flexibility; heavy chains and have a constant region composed of four Ig domains. The variable region of the heavy chain differs in antibodies produced by different B cells, but is the same for all antibodies produced by a single B cell or B cell clone. The variable region of each heavy chain is approximately 110 amino acids long and is composed of a single Ig domain.
CH3
CH
SECTION 1
SS
Fc Region
Light chains
In mammals there are only two types of light chains, which are called lambda () and kappa (). A light chain has two successive domains: one constant domain and one variable domain. The approximate length of a light chain is 211 to 217 amino acids. Each antibody contains two light chains that are always identical; only one type of light chain, or , is present per antibody in mammals. Other types of light chains, such as the iota () chain, are found in lower vertebrates like Chondrichthyes (cartilaginous fishes) and Teleostei (rayfinned fishes).
Fab and Fc regions

Direct-conjugated antibodies are labeled with an enzyme or fluorochrome in the Fc region. The Fc region also anchors the antibody to the plate in ELISA procedures and is also recognized by secondary antibodies in immunoprecipitation, immunoblots and immunohistochemistry. Antibodies can be cleaved into two F(ab) and one Fc fragments by the proteolytic enzyme papain, or into just two parts: one F(ab)2 and one Fc at the hinge region by the proteolytic enzyme pepsin. Fragmenting IgG antibodies is sometimes useful because F(ab) fragments (1) will not precipitate the antigen; and (2) will not be bound by immune cells in live studies because of the lack of an Fc region. Often, because of their smaller size and lack of crosslinking (due to loss of the Fc region), Fab fragments are radiolabeled for use in functional studies. Interestingly, the Fc fragments are often used as blocking agents in histochemical staining.
Antibody Isotypes:
IgG3
SECTION 1
IgM cell
N N
VH VL
IgG1,2+4
light chain or N N
IgD
VL
CH 1
SS
antigen binding
CH CL
SS
1
CH2
IgM
biological activity
C CH2 CH3 C
CHO
S S S S
C
CHO
CL
VH
IgE
CH3 C
heavy chain
IgA
In mammals, antibodies can be divided into five isotypes or classes: IgG, IgM, IgA, IgD and IgE, based on the number of Y units and the type of heavy chain. Heavy chains of IgG, IgM, IgA, IgD, and IgE, are known as gamma (), mu (), alpha (), delta (), and epsilon (), respectively. The isotypes differ in their biological properties, functional locations and ability to deal with different antigens, as depicted in the table below: Class/ subclass IgA1 IgA2 Light chain Molecular weight (kDa)
Heavy chain
Structure
Function Most produced Ig. Found in mucosal areas, such as the gut, respiratory and urogenital tract, and prevents their colonization by pathogens. Resistant to digestion and is secreted in milk. Function unclear; Works with development; mostly B cell bound IgM in B-cell
1 2
or
150 to 600
Monomer to tetramer
IgD
or
150
Monomer
IgE IgG1 IgG2a IgG2b IgG3 IgG4
or
190
Monomer
Binds to allergens and triggers histamine release from mast cells, and is involved in allergy. Also protects against parasitic worms.
1 2 3 4
or
150
Monomer
Major Ig in serum. Provides the majority of antibody based immunity against invading pathogens. Moderate complement fixer (IgG3); can cross placenta.
SECTION 1
IgM
or
900
Pentamer
First response antibody. Expressed on the surface of B cells and in a secreted form with very high avidity. Eliminates pathogens in the early stages of B cell mediated immunity before there is sufficient IgG.
Chicken IgY
There are several advantages to choosing chickens, rather than rabbits or goats to produce polyclonal antibodies. 1. Chickens are not mammals and therefore are more able to make high-avidity antibodies to mammalian antigens (especially highly conserved mammalian proteins). 2. To our knowledge, it is the most ethical way to produce polyclonal antibodies. There is no need to bleed the chickens; simply collect the eggs. 3. A single chicken can produce an enormous amount of antibodies, up to 3 g of IgY per month, which is 10-20 times the amount of a rabbit. Furthermore, compared to rabbits, chickens produce antibodies more quickly. High-titer antibodies are available from eggs as early as day 25. 4. By having the IgY packaged conveniently in eggs, one can collect and store eggs over a long period of time and retroactively purify the IgY from the eggs of desired titer/avidity. 5. It is cheaper to feed and house chickens than rabbits. 6. IgY is a stable antibody sharing the following characteristics with mammalian IgG: Divalent Degraded by papain to yield divalent Fab fragment May be enzyme-labelled, biotinylated and goldlabelled by standard procedures 7. Fc region of chicken IgY is sufficiently different from mammalian IgG: Reduces background by not binding to mammalian rheumatoid factors or other naturally occurring anti-mammalian antibodies (e.g. HAMA) Does not activate mammalian complement systems Does not bind to mammalian Fc receptors Does not bind to Staphylococcal protein A or protein G
SECTION 2: Antibody purification

Centrifugation and filtration are standard laboratory techniques for sample clarification of serum, ascetic fluid and tissue culture supernatant. These techniques remove lipid and particle matter which can block chromatographic columns. For some materials buffer exchange and desalting may also be necessary. Ammonium sulphate precipitation is a further preparation step often used with ascetic fluid to concentrate the immunoglobulins.
Antiserum
Polyclonal antibodies are often available in relatively unpurified formats, described as serum or antiserum. Antiserum refers to the blood from an immunized host from which clotting proteins and red blood cells have been removed. The antiserum will contain antibodies/immunoglobulins of all classes as well as other serum proteins. In addition to antibodies that recognize the target antigen, the antiserum also contains antibodies to various non-target antigens that can sometimes react non-specifically in immunological assays. For this reason, raw antiserum is often purified to eliminate serum proteins and to enrich the fraction of immunoglobulin that specifically reacts with the target antigen.
Tissue culture supernatant

Monoclonal antibodies may be grown as hybridoma cell cultures (cells secreting antibodies) and harvested as hybridoma tissue culture supernatants.
Ascites fluid
Monoclonal antibodies can be produced by growing hybridoma cells within the peritoneal cavity of a mouse (or rat). When injected into a mouse, the hybridoma cells multiply and produce fluid (ascites) in its abdomen. This fluid contains a high concentration of antibody which can be harvested, providing higher antibody yields than hybridoma cell culture.
Antibody purification:
Polyclonal antiserum or monoclonal ascites fluid / tissue culture supernatant is commonly purified by one of three methods:
SECTION 2
Protein A/G purification

Protein A/G purification makes use of the high affinity of Staphylococcus aureus protein A or Streptococcus protein G to the immunoglobulin Fc domain. Protein A/G purification eliminates serum proteins from raw antiserum, but it does not eliminate the non-specific immunoglobulin fraction. Consequently, protein A/G purified antiserum may still possess a small amount of undesirable cross reactivity.
Affinity purification
Affinity purification isolates a specific protein or group of proteins with similar characteristics. The technique separates proteins on the basis of a reversible interaction between the proteins and a specific ligand coupled to a chromatographic matrix. Antigen affinity purification takes advantage of the affinity of the specific immunoglobulin fraction for the immunizing antigen against which it was generated. Antigen affinity purification results in the elimination of the bulk of the non-specific immunoglobulin fraction, while enriching the fraction of immunoglobulin that specifically reacts with the target antigen. The resulting affinity purified immunoglobulin will contain primarily the immunoglobulin of desired specificity.
Pre-absorption
Polyclonal antibodies are sometimes pre-absorbed. This means they have been absorbed with other proteins, or serum from various species, to eliminate any antibody that may cross-react. The resulting purified antibody should be very pure and specific and any crossreactivity should be significantly reduced.
Antibody purification at Abcam:
SECTION 3: Choosing an antibody and antibody dilution

There is often more than one antibody available for any given target. To narrow the range of choice, several aspects of the experiment need to be considered: 1. Type of assay or application 2. Nature of the sample 3. Species of the sample 4. Species of the antibody host 5. Labelling and detection of the antibody The Abcam website has a useful search function. Entering the name of the protein or other target in the search box will generate a list that can be filtered by product type, target, applications tested, species reactivity, host species, clonality, and conjugation. Application Antibody datasheets list the applications that have been tested and found to work. If an application is not listed, this does not mean that the antibody is not suitable. It simply means that it has not been tested and it is unknown how the antibody will perform. When an application has been tested and found not to work, this will be noted on the datasheet. Nature of the sample The nature of the sample will dictate which antibody will work best. At least two aspects need to be considered: 1. The region of the protein one wishes to detect. Antibodies are generated by immunization of host animals with a variety of immunogenic substances including full-length proteins, protein fragments, peptides, whole organisms (for example bacteria), or cells. The immunogen is generally described on the datasheet (though in many cases an exact description of the immunogen is not available for proprietary reasons). If trying to detect a protein fragment or a specific isoform or region of the full-length protein, one needs to be sure to choose an antibody that is raised against an immunogen that is identical to or contained within the fragment or region. If trying to detect a cell surface protein on live cells by FACS, one needs to choose an antibody that is raised against an extracellular domain of the protein.
SECTION 3
2. Processing of the sample. Some antibodies require samples to be processed or treated in a specific manner. For instance, many antibodies will only recognize proteins that have been reduced and denatured, presumably because this reveals epitopes that would otherwise be obscured by secondary and tertiary folding of the proteins. On the other hand, some antibodies will only recognize epitopes on proteins in their native, folded state. (For Abcam antibodies used for western blotting, samples should be reduced and denatured unless otherwise noted on the datasheet). When searching for an antibody for immunohistochemistry, it should be noted that some antibodies are only appropriate for unfixed frozen tissue. For others, an antigen retrieval step that reverses the cross-links introduced by formalin fixation is necessary because they are incapable of binding to their targets in formalin-fixed, paraffin-embedded tissues. These restrictions on use will be noted in the applications section of datasheets. Species of sample The chosen antibody should have been raised against the same species as one is studying, although the antibody may react with the same target protein from other species sharing sufficient amino acid sequence homology. If the sample is not from one of the species listed, this does not mean that the antibody will not detect the protein, but rather that the species has not been tested and we are reluctant to comment on its suitability. A prediction of cross-reactivity can be made based on sequence similarity: Abcam is now proud to have ExPASy and NCBI BLAST links on the datasheets to compare amino acid sequence homology among different species. Choosing the species of primary antibody host In general, the species of the host animal in which an antibody was raised is important when using a conjugated secondary antibody to detect an unconjugated primary. For immunohistochemistry, the primary antibody should be raised in a species as phylogenetically different as possible from the species of the sample. This is to avoid potential cross-reactivity of the secondary anti-immunoglobulin antibody with endogenous immunoglobulins in the sample. For instance, a primary antibody used to detect a protein in a sample from a mouse should not be raised in mouse or rat. A primary antibody raised in rabbit will be a more appropriate choice, followed by an antirabbit IgG secondary antibody conjugated to a detection molecule (enzyme, fluorochrome, biotin, etc.). This issue can be avoided if a conjugated primary antibody is available. For other techniques using samples that do not contain endogenous immunoglobulin, the choice of host species is less critical. An example would be western blotting of a cell lysate that is not expected to contain IgG. However, tissue lysates and tissue culture supernatants that contain serum will contain immunoglobulins. IgG will appear in western blots of reduced, denatured samples as bands at 50 and 25 kDa corresponding to the heavy and light chains of the IgG molecule. Choosing a secondary antibody Secondary antibodies should be raised against the same species as the primary antibody you are using. For example, if your primary is a mouse monoclonal, you will require an anti-mouse secondary. We recommend you check the datasheet of the secondary antibody to ensure it is tested in the application you will be using. Abcam provides a wide range of secondary antibodies conjugated to a range of fluorochromes and chromogens. Check the bottom of the datasheet of the primary antibody you are using. There will be a list of suitable secondary antibodies. To find your own secondary, select this product type using our navigation bar, or by using the links at the center of the homepage. Then choose the species of your primary antibody. This will then give you a range of secondary antibodies for use with that species of primary.
Choosing antibodies for dual staining Double immunostaining of cell cultures or tissue sections using unconjugated primary antibodies requires that those antibodies are raised in different species and that the secondary antibodies recognize one of those species exclusively. Datasheets for secondary antiimmunoglubulin antibodies will state if they have been cross-adsorbed against immunoglobulins from other species to remove those reactivities. Fluorochrome and chromogen labels Labels are conjugated (joined) to antibodies in order to visualize the binding of the antibody. The choice of label depends on several parameters: 1. Detection method: fluorescence or colored precipitate. Fluorescent labels emit light in the visual range when excited by light of a specific wavelength. There are several available, all with their own excitation and emission characteristics. When combined with the appropriate substrate the enzymatic labels HRP and AP form a colored precipitate. 2. Available mounting media (immunohistochemistry only): AEC, Fast Red, INT or any other aqueous chromogen are alcohol soluble and require an aqueous based mounting medium. The others mentioned above are organic, so are best mounted in organic mounting media in order to take advantage of the better refractive index. Fluorescent labels require aqueous mounting media. Phycobiliproteins (phycocyanin / phycoerythrin) require aqueous mounting media with no added glycerol, since this has a quenching effect. 3. Biotinylated antibodies are useful for amplification of signal when followed by an avidin-biotin-enzyme or fluorochrome complex (commonly abbreviated as ABC reagent), or avidin or streptavidin conjugated to an enzyme or fluorochrome.
Unpurified antibody suggested dilutions and concentrations:

Unpurified antibody preparations vary significantly in specific antibody concentration. If the specific antibody concentration of a given unpurified antibody preparation is unknown, one may refer to the following typical ranges as a guideline for estimation:
SECTION 3
Tissue Culture Supernatant WB/dot blot IHC/ICC EIA/ELISA FACS/Flow Cytometry IP Concentration Estimate 1/100 neat to 1/10 1/1000 1/100 1 to 3 mg/ml
Ascites 1/1000 1/100 1/10000 1/1000 1/100 5 to 10 mg/ml
Whole Antiserum 1/500 1/50 to 1/100 1/500 1/500 1/50 to 1/100 1 to 10 mg/ml
Purified Antibody 1 g/ml 5 g/ml 0.1 g/ml 1 g/ml 1 to 10 g/ml
SECTION 4: Fluorescence
4.1 Fluorescence how it works
Due to their novel electronic configurations, fluorochromes have unique and characteristic spectra for absorption (excitation) and emission. A single dye is excited at a particular wavelength and emits a photon at another wavelength. A tandem dye consists of a donor and acceptor fluorochrome molecule, placed in close proximity, allowing for energy transfer between the two. The tandem dye is excited at the excitation wavelength of the acceptor molecule and emits a photon at the emission wavelength of the donor molecule.
Excitation and emission spectral profiles:

Relative Intensity
Laser line (488) Excitation Emission PE
Single (PE)
350
400
450
500
550
600
650
700
750
800
Wavelength (nanometers)
Relative Intensity
Laser line (633) Excitation Emission Cy5
Single (Cy5)
SECTION 4
350
400
450
500
550
600
650
700
750
800
Relative Intensity
Laser line (488) Excitation Emission PE-Cy5
Tandem (PE-Cy5)
350
400
450
500
550
600
650
700
750
800
Energy level diagram - single dye:
Es Excitation 2 3 Fluorescence (Emission)
Laser
Gs
Energy level diagram - tandem dye:
4 Energy transfer Laser 1 Excitation 2 D A 5 Emission
Es D Excitation 2 3 4 A 5 Fluorescence (Emission)
Laser
Gs
SECTION 4
In the case of a single fluorescent dye: 1 A laser set at the signature excitation wavelength for the dye provides electromagnetic energy to an electron in that molecule.
2
The electron moves to an excitation state at the next energy level (Es). Energy is then released in the form of a photon (fluorescence ) and the electron moves back down to the lower energy level (Gs).
In the case of a tandem fluorescent dye: 4 After excitation of the electron by a laser (1-2 above), energy is released by an electron in the donor molecule an electron in the acceptor molecule A .
and is absorbed by
5 The electron in the acceptor molecule moves to an excitation state at the next energy level (Es). Similar to a single dye, energy is then released in the form of a photon (fluorescence) and the electron moves back down to the lower energy level (Gs).
10
4.2 Fluorochrome table:

Fluorochromes Methoxycoumarin Aminocoumarin Pacific blue EviTag quantum dots-Lake Placid Blue Cy2 Chromeo 488 DyLight 488 Alexa Fluor 488 FAM Fluorescein Iso-thiocyanate (FITC) EviTag quantum dots-Adirondack Green HiLyte Fluor 488 EviTag quantum dots-Catskill Green Alexa Fluor 430 Alexa Fluor 532 HEX EviTag quantum dots-Hops Yellow Chromeo 546 Cy3 Alexa Fluor 555 HiLyte Fluor 555 5-TAMRA Alexa Fluor 546 DyLight 549 Phycoerythrin (PE) Tetramethyl Rhodamine Isothiocyanate (TRITC) EviTag quantum dots-Birch Yellow Cy3.5 Rhodamine Red-X PE-Dyomics 590 EviTag quantum dots-Fort Orange ROX Alexa Fluor 568 Red 613 Texas Red PE-Texas Red Alexa Fluor 594 Chromeo 494 Alexa Fluor 633 Allophycocyanin (APC) Quantum Red Alexa Fluor 647 Cy5 Chromeo 642 PE-Cy5 PE-Alexa Fluor 647 PE-Dyomics 647 DyLight 649 HiLyte Fluor 647 Peridinin Chlorophyll (PerCP) Alexa Fluor 660 PE-Cy5.5 APC-Cy 5.5 Cy5.5 TruRed HiLyte Fluor 680 IRDye 700DX Alexa Fluor 680 APC-Cy 7 Cy7 PE-Dyomics 747 HiLyte Fluor 750 PE-Cy7 IRDye 800CW Excitation wavelength 360 350 404 470 489 488 493 495 494 495 505 501 525 434 532 535 545 545 548 555 550 541 556 562 496,566 557 560 576 570 488 585 575 578 480,565 595 566 590 494 632 650 488 650 647 642 565 567 488 654 650 477 663 565 650 675 490,675 678 689 679 650 753 488 753 566 778 Emission wavelength 410 445 456 490 506 517 518 519 519 519 520 527 540 541 554 556 560 561 561 565 566 568 573 576 576 576 580 589 590 599 600 602 603 613 613 616 617 628 647 660 660 665 665 666 666 669 672 673 675 678 690 693 694 694 695 699 700 702 774 775 776 778 778 794 488 FL3,FL5,PM4 595,633,635,647 FL5,FL8,FL9 488 595,633,635,647 647 FL3,FL4,FL6,PM2 FL3,FL4,FL7 488 FL3,FL4,FL6,PM2 488 FL3,FL4,FL6,PM2 595,633,635,647 633,635 FL4,FL7,FL8 FL4,FL8 595,633,635,647 FL4,FL7,FL8 568,543,514 568,543 488 FL2,FL4,PM1 488,514 FL2,FL4,PM1 488 FL1,FL3,PM3 488 FL1,FL3,PM3 488 360,405,407 FL1,FL6 Excitation laser lines (nm) Fluorescence channel
SECTION 4
11
Nucleic acid probes:

Nucleic Acid Dyes Hoechst 33342 Hoechst 33258 DAPI SYTOX Blue YOYO-1 SYTOX Green TOTO-1, TO-PRO-1 Mithramycin SYTOX Orange Chromomycin A3 Ethidium Bromide Propidium iodide (PI) Excitation wavelength 350 352 359 431 491 504 509 450 547 445 493 305, 540 Emission wavelength 461 461 461 480 509 523 533 570 570 575 620 620 325,360,488 FL3,FL4,PM1 325,360,405,407 FL1,FL6 Excitation laser lines (nm) Fluorescence channel
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SECTION 5: Western blotting

Western blotting is a technique that identifies specific proteins in a given sample or extract after their separation using polyacrylamide gel electrophoresis. The polyacrylamide gel is placed adjacent to a membrane, which is typically nitrocellulose or PVDF (polyvinylidene fluoride), and the application of an electrical current induces the proteins to migrate from the gel to the membrane on which they become immobilized. The membrane is then a replica of the gel protein and can subsequently be stained with an antibody. The following western blotting protocol includes the process of sample preparation, gel electrophoresis, transfer from gel to membrane, and immunostaining for protein detection. Protocols may require optimization according to the electrophoresis and transfer equipment used and readers are advised to consult the specific manufacturers instructions.
Western blot
Sample preparation
Lysis of sample in appropriate lysis buffer (eg. RIPA) Protein assay to determine protein concentration
Reduce and denature sample (unless stated otherwise on antibody datasheet) Add sample buffer (SDS and mercaptoethanol). Heat 95C 5 min
Loading the gel
20 - 30 g whole lysate per lane or 100 ng purified protein Optimize amount depending on expression level of the protein
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Prepare running buffer Assemble the gel in the tank
Running the gel
-ve
100 V - 150 V for 50 - 90 min Optimize time and voltage Follow manufacturers instructions Gel percentage depends on size of protein: 4-40 kDa 20% 12-45 kDa 15% 10-70 kDa 12.5% 15-100 kDa 10% 25-200 kDa 8%
Smaller proteins (negatively charged) move more quickly through the gel towards the positive cathode. Proteins separate out according to size.
+ve
Transfer proteins from the gel to membrane
Prepare transfer buffer Cut a piece of membrane and wet in methanol Transfer the membrane to 1 x transfer buffer Assemble transfer stack
+ve
+
Sponge Filter Paper Membrane Gel Filter Paper Sponge
100 V - 60 - 120 min 4C Optimize time and voltage Follow manufacturers instructions Negatively charged proteins move up towards the positive cathode and onto the membrane.
Current
-ve
(Continued Overleaf)
13
Western blot (continued)

Check the transfer Ponceau red staining of the membrane or Coomassie staining of the gel
Blocking Primary antibody incubation
Incubate membrane in 5% milk or BSA for 1 to 2 hr For detection of phospho proteins, use BSA instead of milk
Band of protein / antigen on membrane
Incubate membrane in primary antibody (diluted in PBS 0.2% Tween 20. 2 - 5% BSA) 1-2 hr RT or 4C overnight at recommended concentration
Secondary antibody incubation

Incubate with enzyme (eg. HRP) conjugated secondary Antibody (diluted in eg PBS 0.2% Tween 20. 2 - 5% BSA) 1-3 hr RT at recommended concentration
Key
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Detection (eg. ECL detection)
Substrate eg Hydrogen peroxide + luminol 3-aminophtalate (light sensitive product) Antigen
Primary antibody
Conjugated Secondary antibody
Scan and analyze results
5.1. Sample preparation

1. 2. 3. 4. 5. 6. Lysis buffers Protease and phosphatase inhibitors Preparation of lysate from cell culture Preparation of lysate from tissues Determination of protein concentration Preparation of samples for loading into gels
5.2. Electrophoresis
1. 2. 3. 4. 5. Preparation of PAGE gels Positive controls Molecular weight markers Loading samples and running the gel Use of loading controls
5.3. Transfer of proteins and staining (western blotting)

1. Visualization of proteins in gels 2. Transfer 3. Visualization of proteins in membranes: Ponceau Red 4. Blocking the membrane 5. Incubation with the primary antibody 6. Incubation with the secondary antibody 7. Development methods
5.4. References 5.5. Troubleshooting tips
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5.1. Sample preparation

1. Lysis buffers To prepare samples for running on a gel, cells and tissues need to be lysed to release the proteins of interest. This solubilizes the proteins so they can migrate individually through a separating gel. There are many recipes for lysis buffers but a few will serve for most western blotting experiments. In brief, they differ in their ability to solubilize proteins, with those containing sodium dodecyl sulfate and other ionic detergents considered to be the harshest and therefore most likely to give the highest yield. Most Abcam antibodies recognize reduced and denatured protein and should be used under reducing and denaturing conditions. It is important to note though that some antibodies will only recognize a protein in its native, non-denatured form and will not recognize a protein that has been extracted with a denaturing detergent (SDS, deoxycholate, and somewhat less denaturing, Triton X-100 and NP-40). The main consideration when choosing a lysis buffer is whether the antibody one has chosen will recognize denatured samples. When this is not the case, it will be noted on the antibody datasheet, and buffers without detergent or with relatively mild non-ionic detergents (NP-40, Triton X-100) should be used. Protein location and lysis buffer choice For buffer recipes, please see the buffers section 11 beginning on page 77.
Sample type Whole cell Cytoplasmic (soluble) Cytoplasmic (cytoskeletal bound) Membrane bound Nuclear Mitochondria
Lysis buffer NP-40 or RIPA Tris-HCl Tris-Triton NP-40 or RIPA RIPA or use nuclear fraction protocol* RIPA or use mitochondrial fraction protocol*
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*Proteins that are found exclusively or predominantly in a sub-cellular location can be enriched in a lysate of the sub-cellular fraction compared to whole cell or tissue lysates. This can be useful when trying to obtain a signal for a weakly-expressed protein. For instance, a nuclear protein will be a larger proportion of the total protein in a nuclear lysate than it will be in a whole-cell or whole-tissue lysate, making it possible to load more of the protein per gel lane. Another advantage is the removal of potentially cross-reactive proteins present in the unused fractions. Please consult our separate protocols for sub-cellular fractionation. Nonidet-P40 (NP40) buffer. This is a popular buffer for studying proteins that are cytoplasmic, or membrane-bound, or for whole cell extracts. If there is concern that the protein of interest is not being completely extracted from insoluble material or aggregates, RIPA buffer may be more suitable, as it contains ionic detergents that may more readily bring the proteins into solution. RIPA buffer (Radio Immuno Precipitation Assay buffer) is also useful for whole cell extracts and membrane-bound proteins, and may be preferable to NP-40 or Triton X-100-only buffers for extracting nuclear proteins than buffers containing only NP-40 or Triton X-100. It will disrupt protein-protein interactions and may therefore be problematic for immunoprecipitations/pull down assays. In cases where it is important to preserve protein-protein interactions or to minimize denaturation (for example, when it is known that the antibody to be used will only recognize a non-denatured epitope), a buffer without ionic detergents (e.g. SDS) and ideally without nonionic detergents (e.g. Triton X-100) should be used. Cell lysis with detergent-free buffer is achieved by mechanical shearing, often with a Dounce homogenizer or by passing cells through a syringe tip. In these cases a simple Tris buffer will suffice, but as noted above, buffers with detergents are required to release membrane- or cytoskeleton- bound proteins.
15
2. Protease and phosphatase inhibitors As soon as lysis occurs, proteolysis, de-phosphorylation and denaturation begin. These events can be slowed down tremendously if samples are kept on ice or at 4C at all times and appropriate inhibitors are added fresh to the lysis buffer. Ready-to-use cocktails of inhibitors from various suppliers are available but you can make your own cocktail. Inhibitor Protease/phosphatase inhibited Trypsin, Chymotrypsin, Plasmin Lysosomal Aspartic proteases Serine, Cysteine proteases Metalloproteases that require Mg++ and Mn++ Metalloproteases that require Ca++ Serine/Threonine phosphatases Tyrosine phosphatases Final concentration in lysis buffer 2 g/ml 5-10 g/ml 1 g/ml 1 mM 5 mM 1 mM 5-10 mM 1 mM Stock (store at -20C) Dilute in water, 10 mg/ml. Do not re-use once defrosted Dilute in water. Do not re-use once defrosted. Dilute in methanol, 1 mM. Dilute in ethanol. You can reuse the same aliquot. Dilute in H2O 0.5 M. Adjust pH to 8.0. Dilute in H2O 0.5 M. Adjust pH to 8.0. Dilute in water. Do not re-use once defrosted. Dilute in water. Do not re-use once defrosted.
Aprotinin Leupeptin Pepstatin A PMSF EDTA EGTA Na Fluoride
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Na Orthovanadate
Sodium orthovanadate preparation All steps to be performed in a fume hood. 1. Prepare a 100 mM sodium orthovanadate solution in double distilled water. 2. Set pH to 9.0 by addition of HCl. 3. Boil until colorless. Minimize volume change due to evaporation by covering loosely. 4. Cool to room temperature. 5. Set pH to 9.0 again. 6. Boil again until colorless. 7. Repeat this cycle until the solution remains at pH 9.0 after boiling and cooling. 8. Bring up to the initial volume with water. 9. Store in aliquots at - 20C. Discard if samples turn yellow. 3. Preparation of lysate from cell culture 1. Place the cell culture dish in ice and wash the cells with ice-cold PBS. 2. Drain the PBS, then add ice-cold lysis buffer (1 ml per 107 cells/100 mm2 dish/150 cm2 flask; 0.5ml per 5x106 cells/60 mm2 dish/75 cm2 flask). 3. Scrape adherent cells off the dish using a cold plastic cell scraper, then gently transfer the cell suspension into a pre-cooled micro centrifuge tube. 4. Maintain constant agitation for 30 min at 4C. 5. Spin at 16,000 x g for 20 min in a 4C pre-cooled micro centrifuge. 6. Gently remove the tubes from the micro centrifuge and place on ice. Transfer the supernatant to a fresh tube kept on ice, and discard the pellet. 4. Preparation of lysate from tissues 1. Dissect the tissue of interest with clean tools, on ice preferably, and as quickly as possible to prevent degradation by proteases. 2. Place the tissue in round-bottom micro centrifuge tubes or Eppendorf tubes and immerse in liquid nitrogen to snap freeze. Store samples at -80C for later use or keep on ice for immediate homogenization. For a ~5 mg piece of tissue, add ~300 l lysis buffer rapidly to the tube, homogenize with an electric homogenizer, rinse the blade twice with another 2 X 300 l lysis buffer, then maintain constant agitation for 2 hr at 4C (e.g. place on an orbital shaker in the fridge). Volumes of lysis buffer must be determined in relation to the amount of tissue present. Protein extract should not be too dilute, to avoid the need to load large volumes per gel lane. The minimum protein concentration is 0.1 mg/ml; optimal concentration is 1-5 mg/ml).
16
3. Centrifuge for 20 min at 16,000 x rpm at 4C in a microcentrifuge for 20 min. Gently remove the tubes from the centrifuge and place on ice. Transfer the supernatant to a fresh tube kept on ice; discard the pellet.
The buffer (with inhibitors) should be ice-cold prior to homogenization.
5. Determination of protein concentration Perform a Bradford, Lowry, or BCA assay. Bovine serum albumin (BSA) is a frequently-used protein standard. Once you have determined the concentration of each sample, you can freeze them at -20C or -80C for later use or prepare for immunoprecipitation or for loading onto a gel. 6. Preparation of samples for loading into gels: denatured and native, reduced and non-reduced. a) Denatured, reduced samples Antibodies typically recognize a small portion of the protein of interest (referred to as the epitope) and this domain may reside within the 3D conformation of the protein. To enable access of the antibody to this portion it is necessary to unfold the protein, i.e. denature it. To denature the protein, use a loading buffer with the anionic denaturing detergent sodium dodecyl sulfate (SDS), and boil the mixture at 95-100C for 5 min. Heating at 70C for 5-10 min is also acceptable and may be preferable when studying trans-membrane proteins. These tend to aggregate when boiled and the aggregates may not enter the gel efficiently. The standard loading buffer is called 2 X Laemmli buffer, first described in Nature, 1970 Aug 15;227(5259):680-5. It can also be made at 4 X and 6 X strength to minimize dilution of the samples. The 2 X stock solution is mixed in a 1:1 ratio with the sample.
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When SDS is used with proteins, all of the proteins become negatively charged by their attachment to the SDS anions. SDS denatures proteins by wrapping around the polypeptide backbone. SDS binds to proteins fairly specifically in a mass ratio of 1.4:1. In so doing, SDS confers a negative charge to the polypeptide in proportion to its length i.e. the denatured polypeptides become rods of negatively charged clouds with equal charge or charge densities per unit length. In denaturing SDS-PAGE separations, therefore, migration is determined not by intrinsic electrical charge of the polypeptide, but by molecular weight. SDS grade is of utmost importance: a protein stained background along individual gel tracts with indistinct protein bands are indicative of old or poor quality SDS. It is usually necessary to reduce disulphide bridges in proteins before they adopt the random-coil configuration necessary for separation by size by adding -mercaptoethanol or dithiothreitol (DTT). Glycerol is added to the loading buffer to increase the density of the sample to be loaded and hence maintain the sample at the bottom of the well, restricting overflow and uneven gel loading. To enable visualization of the migration of proteins it is common to include a small anionic dye molecule (e.g. bromophenol blue in the loading buffer. The dye will migrate the fastest of any component in the mixture to be separated and provide a migration front to monitor the separation progress. During protein sample treatment, vortexing before and after the heating step is required for the best resolution. b) Native and non-reduced samples Alternatively, an antibody may recognize an epitope made up of non-contiguous amino acids in their native conformation. Although the amino acids of the epitope are separated from one another in the primary sequence, they can be closer to each other in the threedimensional structure of the protein. The antibody will only recognize the epitope as it exists on the surface of the folded structure. It is imperative in these circumstances to run a western blot in non-denaturing conditions, and this will be noted on the datasheet in the applications section. In general, a non-denaturing condition simply means leaving SDS out of the sample and migration buffers and not heating the samples. Certain antibodies only recognize protein in its non-reduced form i.e. in an oxidized form (particularly on cysteine residues) and the reducing agents -mercaptoethanol and DTT must be left out of the loading buffer and migration buffer (non reducing conditions).
17
Protein State Reduced - Denatured Reduced - Native Oxidized - Denatured Oxidized - Native
Gel condition Reducing & Denaturing Reducing & Non-Denaturing Non-Reducing & Denaturing Non-reducing & Native
Loading buffer With -mercaptoethanol or DTT and SDS With -mercaptoethanol or DTT, no SDS No -mercaptoethanol or DTT, with SDS, No -mercaptoethanol or DTT, no SDS,
Migration buffer With SDS No SDS With SDS No SDS
Rule of thumb: Reduce and denature unless the datasheet specifies otherwise.
5.2. Electrophoresis
Electrophoresis can be one dimensional (i.e., one plane of separation) or two dimensional. One dimensional electrophoresis is used for most routine protein and nucleic acid separations. Two dimensional separation of proteins is used for finger-printing (i.e., analysis of total protein content), and when properly constructed can be extremely accurate in resolving all of the proteins present within a cell. Here we will be describing techniques for one dimensional electrophoresis. We recommend Gel Electrophoresis of Proteins: A Practical Approach (3rd Edition, B.D. Hames and D. Rickwood, The Practical Approach Series, Oxford University Press, 1998) as a reference for basic understanding of 2D electrophoresis protocols. 1. Preparation of PAGE gels When separated on a polyacrylamide gel, the procedure is abbreviated as SDS-PAGE (for Sodium Dodecyl Sulfate PolyAcrylamide Gel Electrophoresis). The technique is a standard means for separating proteins according to their molecular weight. Polyacrylamide gels are formed from the polymerization of two compounds, acrylamide and N,N-methylenebis-acrylamide (Bis, for short). Bis is a cross-linking agent for the gels. The polymerization is initiated by the addition of ammonium persulfate along with either DMAP or TEMED. The gels are neutral, hydrophilic, three-dimensional networks of long hydrocarbons crosslinked by methylene groups. The separation of molecules within a gel is determined by the relative size of the pores formed within the gel. The pore size of a gel is determined by two factors: the total amount of acrylamide present (designated as %T) and the amount of cross-linker (%C). As the percentage of acrylamide increases, the pore size decreases. 5%C gives the smallest pore size. Any increase or decrease in %C increases or decreases the pore size. Gels are designated as percent solutions and will have two necessary parameters. The total acrylamide is given as a percentage (w/v) of the acrylamide plus the bis-acrylamide. Thus, a 7.5%T would indicate that there is a total of 7.5 g of acrylamide and bis per 100 ml of gel.
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Running the gel
-ve
100 V - 150 V for 50 - 90 min Optimize time and voltage Follow manufacturers instructions Gel percentage depends on size of protein: 4-40 kDa 20% 12-45 kDa 15% 10-70 kDa 12.5% 15-100 kDa 10% 25-200 kDa 8%
Smaller proteins (negatively charged) move more quickly through the gel towards the positive cathode. Proteins separate out according to size.
+ve
Gels can be purchased ready-made from commercial sources or produced in the laboratory (recipes can be found in laboratory handbooks). The percentage of the gel is critical to the rate of migration and degree of separation between proteins.
18
Rule of thumb: The smaller the size of the protein of interest, the higher the percentage of mono/bis. The bigger the size of the protein of interest, the lower the percentage of mono/bis.
Protein size (kDa) 4-40 12-45 10-70 15-100 25-200
Gel percentage (%) 20 15 12.5 10 8
Acrylamide is a potent cumulative neurotoxin: wear gloves at all times. Place gels in the electrophoresis tank as instructed by the manufacturer and bathe in migration buffer. 2. Positive controls A positive control lysate is used to demonstrate that the protocol is efficient and correct and that the antibody recognizes the target protein which may not be present in the experimental samples.
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We strongly recommend the use of a positive control lysate when setting up a new experiment; this will give you immediate confidence in the protocol.
3. Molecular weight markers A range of molecular weight markers run alongside the samples will enable the determination of the protein size (see below) and allow you to monitor the progress of an electrophoretic run. There are many commercially available MW markers. Abcam has the following molecular weight markers: Catalogue ID ab41746 (MW 116, 97.4, 66, 45, 36 29, 24, 20.1, 14.2 kDa) Catalogue ID ab48854 (MW 70, 57, 40, 28, 18, 13.5 and 8.5 kDa) 4. Loading samples and running the gel Use special gel loading tips or a micro-syringe to load the complete sample in a narrow well. Take care not to pierce base of the well with the tip as this will create a distorted band. Never overfill wells, this could lead to poor data if samples spill into adjacent wells and poorly resolved bands. Load 20-40 g total protein per mini-gel well. The gels will be submerged in migration buffer which normally contains SDS, except in native gel electrophoresis. A standard migration buffer (also called running buffer) for PAGE is 1 X Tris-glycine (See Buffers section beginning on page 77). Run the gel for the recommended time as instructed by the manufacturer. This can vary from machine to machine (1 hr to overnight depending on the voltage). When the dye molecule (the migration front) reaches the bottom of the gel, the power is turned off. Proteins will slowly elute from the gel at this point, so do not store the gel and proceed immediately to transfer.
19
5. Loading controls Loading controls are required to check that the lanes in your gel have been evenly loaded with sample. This is important especially when a comparison must be made between the expression levels of a protein in different samples. They are also useful to check for even transfer from the gel to the membrane across the whole gel. Where even loading or transfer have not occurred, the loading control bands can be used to quantify the protein amounts in each lane. For publication-quality work, use of a loading control is absolutely essential. Molecular weight (kDa)
Loading control
Sample type
Caution Not suitable for skeletal muscle samples. Changes in cell-growth conditions and interactions with extracellular matrix components may alter actin protein synthesis (Farmer et al, 1983). Some physiological factors, such as hypoxia and diabetes, increase GAPDH expression in certain cell types. Tubulin expression may vary according to resistance to antimicrobial and antimitotic drugs (Sangrajrang S. et al, 1998, Prasad V et al, 2000). Many proteins run at the same 16 kDa size as COXIV. Not suitable for samples where the nuclear envelope is removed. Not suitable for samples where DNA is removed.
Beta Actin
Whole cell / cytoplasmic Whole cell / cytoplasmic Whole cell / cytoplasmic Mitochondrial Mitochondrial Nuclear Nuclear
43
GAPDH Tubulin VDCA1/Porin COXIV Lamin B1 TATA binding protein TBP
30-40 55 31 16 66 38
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5.3. Transfer of proteins and staining

1. Visualization of proteins in gels This visualization of protein at this stage is useful to determine if proteins have migrated uniformly and evenly. Use the copper stain if you plan to transfer the separated proteins to a membrane, as the Coomassie stain is not reversible. Only use the Coomassie stain on gels post-transfer to check the efficiency of the transfer, or if you have no plans to transfer and just want to observe the results of the SDSPAGE separation. a) Coomassie stain As soon as the power is turned off the separated protein bands will begin to diffuse as they are freely soluble in aqueous solution. To prevent diffusion, treat the gel with a 40% distilled water, 10% acetic acid, and 50% methanol solution which causes almost all proteins to precipitate (become insoluble). To visualize the fixed proteins place the gel in the same mixture but with the addition of 0.25% by weight Coomassie Brilliant Blue R-250. Incubate 4 hr to overnight at room temperature on a shaker. Transfer the gel (save the dye mixture; it can be re-used many times) to a mixture of 67.5% distilled water, 7.5% acetic acid, and 25% methanol, place on shaker, and replace with fresh rinse mixture until the excess dye has been removed. The stain will not bind to the acrylamide, and will wash out to leave a clear gel). The bands of proteins in the gel take on a deep blue color from the stain. b) Copper Stain Briefly rinse freshly electrophoresed gels in distilled water (30 sec maximum) and then transfer to 0.3 M CuCl2 for 5 to 15 min. Wash the gels for a short time in de-ionized water, and view them against a dark-field background. Proteins come up as clear zones in a translucent blue background. Gels may be destained completely by repeated washing in 0.1- 0.25 M Tris/0.25 M EDTA pH 8.0. Move the gel to a dish of transfer buffer before proceeding with transfer according to the transfer apparatus manufacturers instructions. Transfer 1. Detailed instructions for the transfer process can be found on the websites of the manufacturers of transfer apparatus, and will vary depending on the system. The principle for transfer is the migration of proteins upon application of an electrical charge from the gel onto a membrane. 2. Transfer can be done in wet or semi-dry conditions. Semi-dry transfer is generally faster but wet transfer is less prone to failure due to drying of the membrane and is especially recommended for large proteins, >100 kDa. For both kinds of transfer the membrane is placed next to the gel. The two are sandwiched between absorbent materials, and clamped between solid supports to maintain tight contact between the gel and membrane. 3. In wet transfer, the gel and membrane are sandwiched between sponge and paper (sponge/paper/gel/membrane/paper/sponge) and all are clamped tightly together after ensuring no air bubbles have formed between the gel and membrane. The sandwich is submerged in transfer buffer to which an electrical field is applied. The negatively-charged proteins travel towards the positively-charged electrode,
20
but the membrane stops them, binds them, and prevents them from continuing on. As a guideline, the gel should be run for 1 to 2 hr at 100V. However, this time and voltage may require some optimization. We recommend that you follow manufacturers instructions.
+ve
+
Sponge Filter Paper Membrane Gel Filter Paper Sponge
100 V 60 -120 min 4C Optimize time and voltage Follow manufacturers instructions Negatively charged proteins move up towards the positive cathode and onto the membrane.
Current
-ve
4. A standard buffer for wet transfer is the same as the 1 X Tris-glycine buffer used for the migration/running buffer without SDS but with the addition of methanol to a final concentration of 20%. For proteins larger than 80 kDa, it is recommended that SDS is included at a final concentration of 0.1%. 5. In semi-dry transfer, a sandwich of paper/gel/membrane/paper wetted in transfer buffer is placed directly between positive and negative electrodes (cathode and anode respectively). As for wet transfer, it is important that the membrane is closest to the positive electrode and the gel closest to the negative electrode. The proportion of Tris and glycine in the transfer buffer is not necessarily the same as for wet transfer; consult the apparatus manufacturers protocol. A standard recipe is 48 mM Tris, 39 mM glycine, 0.04% SDS, 20% methanol.
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6. Two types of membranes are available: nitrocellulose and PVDF (positively-charged nylon). Both work well. PVDF membranes require careful pre-treatment: cut the membrane to the appropriate size then soak it in methanol for 1-2 min. Incubate in ice cold transfer buffer for 5 min. The gel needs to equilibrate for 3-5 min in ice cold transfer buffer. Failure to do so will cause shrinking while transferring, and a distorted pattern of transfer.
Note on transfer of large and small proteins

The balance of SDS and methanol in the transfer buffer, protein size, and gel percentage can affect transfer efficiency. The following modifications will encourage efficient transfer. Large proteins (>100 kDa) 1. For large proteins, transfer out of the gel may be very slow, just as they run slowly within the gel during separation. If blotting a large protein, be sure to run your samples in a low-concentration gel, 8% or less. These will be very fragile, so handle carefully. 2. Large proteins will tend to precipitate in the gel, hindering transfer. Adding SDS to a final concentration of 0.1% in the transfer buffer will discourage this. Methanol tends to remove SDS from proteins, so reducing the methanol percentage to 10% or less will also guard against precipitation. 3. Lowering methanol in the transfer buffer also promotes swelling of the gel, allowing large proteins to transfer more easily. 4. Methanol is only necessary if using nitrocellulose. If using PVDF, methanol can be removed from the transfer buffer altogether, and is only needed to activate the PVDF before assembling the gel/membrane sandwich. 5. Choose wet transfer overnight at 4C instead of semi-dry transfer. Small proteins (<100 kDa) 1. All proteins are hindered from binding to membranes by SDS but small proteins more so than large proteins. If your protein of interest is small, consider removing SDS from the transfer buffer. 2. Keep the methanol concentration at 20%. The following reference discusses a gel and buffer system that allows transfer of proteins as large as 500 kDa: Bolt and Mahoney, High-efficiency blotting of proteins of diverse sizes following sodium dodecyl sulfatepolyacrylamide, gel electrophoresis. Analytical Biochemistry 247, 185192 (1997).
21
More transfer tips: Avoid touching the membrane with your fingers; use tweezers instead. Oils and proteins present on fingers will block efficient transfer and create dirty blots. After sandwiching the gel and membrane between paper, air bubbles between the gel and membrane can be removed by rolling them out with a pipet or 15 ml tube, or by assembling the sandwich in a dish of transfer buffer to prevent formation of bubbles in the first place. Wear gloves! Make sure the paper and membrane are cut to the same size as the gel. Large overhangs may prevent a current from passing through the membrane in semi-dry transfers. Chicken antibodies tend to bind PVDF and other nylon-based membranes, leading to high background. Switching to a nitrocellulose membrane should help reduce background staining.
3. Visualization of proteins in membranes: Ponceau Red To check the success of transfer, wash the membrane in TBST (for a TBST recipe, see Buffers section 11 page 77). Prepare a stock of 2% Ponceau S in 30% trichloroacetic acid and 30% sulfosalicylic acid. Incubate on an agitator for 5 min. Then dilute the stock 1:10. Wash the membrane extensively in water until the water is clear and the protein bands are well-defined. The membrane may be destained completely by repeated washing in TBST or water. When using a PVDF membrane, re-activate the membrane with methanol then wash again in TBST.
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4. Blocking the membrane Two blocking solutions are traditionally used: non-fat milk or BSA (Cohn fraction V). Milk is cheaper but is not recommended for studies of phospho-proteins (milk contains casein which is a phospho-protein; it causes high background because the phospho-specific antibody detects the casein present in the milk). Blocking the membrane prevents non-specific background binding of the primary and/or secondary antibodies to the membrane. Some antibodies give a stronger signal on membranes blocked with BSA as opposed to milk. Check the application notes on the datasheet in case there are specific instructions on how to block the membrane. Incubate in blocking buffer for 1 hr at 4C with agitation. Rinse for 5 seconds in TBST after the incubation. 5. Incubation with the primary antibody Incubation buffer: Dilute the antibody in TBST at the suggested dilution. If the datasheet does not have a recommended dilution test a range (1:100-1:3000) and choose one based on the results. Too much antibody will result in non-specific bands. It is traditional in certain laboratories to incubate the antibody in blocking buffer, while other laboratories incubate the antibody in TBST without a blocking agent. The results are variable from antibody to antibody and you may find it makes a difference to either use no blocking agent in the antibody buffer or the same agent as the blocking buffer.
If high background is not an issue, some antibodies produce a much stronger signal if diluted in buffer with low concentrations (0.5 0.25%) of milk or BSA, or none at all.
Incubation time: The time can vary between a few hours and overnight (rarely more than 18 hr), and is dependent on the binding affinity of the antibody for the protein and its abundance. We recommend a more dilute antibody and a prolonged incubation to ensure specific binding. Incubation temperature: If incubating in blocking buffer overnight, it is imperative to incubate at 4C or contamination will cause degradation of the protein (especially phospho groups). Agitation of the antibody is recommended to enable adequate homogenous covering of the membrane and prevent uneven binding. 6. Incubation with secondary antibody Wash the membrane several times in TBST while agitating for 5 min or more per wash to remove residual primary antibody.
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Incubation buffer and dilution: Dilute the antibody in TBST at the suggested dilution. If the datasheet does not have a recommended dilution, try a range (1:1000- 1:20,000) and optimize according to the results. Too much antibody will result in non-specific bands. You may incubate the secondary antibody (and primary antibody) in blocking buffer, but a reduction in background may come at the cost of a weaker specific signal, presumably because the blocking protein hinders binding of the antibody to the target protein. Incubation time and temperature: 1-2 hr at room temperature with agitation. Which conjugate? We recommend HRP-conjugated secondary antibodies. ALP-conjugated secondary antibodies (alkaline phosphatase) are not recommended as they are less sensitive. 7. Development methods Detection kits: For HRP-conjugated antibodies: ECL and ECL+ (home made or commercially available) are the traditional kits used and we recommend ECL+. For the new generation detection machines such as Genegnome, use the detection kit recommended by the manufacturer of the machine. We do not recommend ECL or BCIP/NBT detection kits as they are not as sensitive. X-ray films: Manual film development is traditionally used and enables the scientist to control the incubation time of the x-ray film in the developing agent and fixation agent. Automated x-ray film developers are also widely used and easy to use.
Remember that an over-exposed film is not suitable for analysis as determination of the relative amount of protein is not possible. Overexposed films show totally black bands with no contrast, and/or numerous non-specific bands.
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Digital images: The new generation of film developers are units with a camera inside an enclosure, removing the need for a darkroom. The camera detects the chemiluminescence emanating from the membrane, transforming the signal into a digital image for rapid analysis with software. A range of machines are now commercially available. At the front of the next generation are systems which do not use HRP-conjugated antibodies (i.e. chemiluminescence). For example, STORM analyzers detect fluorescence from fluorochrome-conjugated secondary antibodies. The Odyssey Infrared Imaging System detects infrared fluorescence.
5.4. References
Harlow, Ed, and David Lane. Using Antibodies. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, 1999. B.D. Hames and D. Rickwood. Gel Electrophoresis of Proteins: A Practical Approach 3rd Edition, The Practical Approach Series, Oxford University Press, 1998. Bolt and Mahoney, High-efficiency blotting of proteins of diverse sizes following sodium dodecyl sulfatepolyacrylamide, gel electrophoresis. Analytical Biochemistry 247, 185192 (1997).
5.5. Troubleshooting tips western blotting

No signal The primary antibody and the secondary antibody are not compatible. Use secondary antibody that was raised against the species in which the primary was raised (e.g.primary is raised in rabbit, use antirabbit secondary). Not enough primary or secondary antibody is bound to the protein of interest. Use more concentrated antibody. Incubate longer (e.g. overnight) at 4C. Cross-reaction between blocking agent and primary or secondary antibody. Use a mild detergent such as Tween 20 or switch blocking reagent (i.e. commonly used blocking reagents are milk, BSA, serum or gelatin). The primary antibody does not recognize the protein in the species being tested. Check the datasheet or perform an alignment of the immunogen sequence with the sequence of the protein you are trying to detect to ensure your antibody should react with the target protein. Run the recommended positive control.
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Insufficient antigen. Load at least 20-30 g protein per lane. Use protease inhibitors. Run the recommended positive control. The protein of interest is not abundantly present in the tissue. Use an enrichment step to maximize the signal (e.g. prepare nuclear lysates for a nuclear protein, etc.). Poor transfer of protein to membrane. Check the transfer with a reversible stain such as Ponceau S. Check that the transfer was not performed the wrong way. Lift using PVDF membrane making sure you pre-soak the membrane in MeOH then in transfer buffer. Excessive washing of the membrane. Do not over wash the membrane. Too much blocking does not allow you to visualize your protein of interest. Instead of using 5% milk in the antibody buffers try removing the milk or using 0.5%. Switch blocking reagents or block for less time. Over-use of the primary antibody. Use fresh antibody as the effective concentration is lowered upon each re-use of the diluted, working solution. Secondary antibody inhibited by sodium azide. Do not use sodium azide together with HRP-conjugated antibodies. Detection kit is old and substrate is inactive. Use fresh substrate.
High background SECTION 5

Blocking of non-specific binding might be absent or insufficient. Increase the blocking incubation period and consider changing blocking agent. Abcam recommends 5% non-fat dry milk, 3% BSA, or normal serum for 30 min. These can be included in the antibody buffers as well. The primary antibody concentration may be too high. Titrate the antibody to the optimal concentration. Incubate for longer but in more dilute antibody (a slow but targeted binding is best). Incubation temperature may be too high. Incubate blot at 4C. The secondary antibody may be binding non-specifically or reacting with the blocking reagent. Run a secondary control without primary antibody. Cross-reaction between blocking agent and primary or secondary. Add a mild detergent such as Tween 20 to the incubation and washing buffer. Milk contains casein which is a phosphoprotein. Phospho specific antibodies can cross react with milk the caseinin the milk solution and causing high background. Use BSA as a blocking reagent instead of milk. Washing of unbound antibodies may be insufficient. Increase the number of washes. Your choice of membrane may give high background. Nitrocellulose membrane is considered to give less background than PVDF. The membrane has dried out. Care should be taken to prevent the membrane from drying out during incubation . Ensure the membrane is covered with enough buffer at all stages and place a rotator or on gentle agitation to ensure membrane is gently washed in the solution.
Multiple bands
Cell lines that have been frequently passaged gradually accumulate differences in their protein expression profiles. Go back to the original non-passaged cell line and run the current and original cell line samples in parallel. The protein sample has multiple modified forms in vivo such as acetylation, methylation, myristylation, phosphorylation, glycosylation etc. Examine the literature and use an agent to dephosphorylate, de-glycosylate your samples to demonstrate post-translation modifications. The target in your protein sample has been digested (more likely if the bands are of lower molecular weight). Make sure that you incorporate sufficient protease inhibitors in your sample buffer.
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Unreported novel proteins or different splice variants that share similar epitopes and could possibly be from the same protein family are being detected. Check the literature for other reports and also perform a BLAST search. Use the cell line or tissue reported on the datasheet. Primary antibody concentration is too high - at high concentration multiple bands are often seen. Try decreasing the antibody concentration and/or the incubation period. Secondary antibody concentration is too high - at high concentration secondaries will bind nonspecifically. Try decreasing the concentration. Run a secondary antibody control (without the primary). The antibody has not been purified. Try to use affinity purified antibody. This will often remove non-specific bands. The bands may be non-specific. Where possible use blocking peptides to differentiate between specific and non-specific bands. Only specific bands should be blocked and thus disappear. The protein target may form multimers. Try boiling in SDS-Page for 10 min rather than 5 min to disrupt multimers.
Uneven white spotson the blot

Air bubbles were trapped against the membrane during transfer or the antibody is not evenly spread on the membrane. Make sure you remove bubbles when preparing the gel for transfer. Incubate antibodies under agitation.
Black dots on the blot

The antibodies are binding to the blocking agent. Filter the blocking agent.
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White bands on a black blot (negative of expected blot)

Too much primary and/or too much secondary antibody. Dilute the antibodies more.
MW marker lane is black

The antibody is reacting with the MW marker. Add a blank lane between the MW marker and the first sample lane.
The band of interest is very low/high on the blot

Separation is not efficient. Change the gel percentage: a higher percentage for small protein, lower percentage for large proteins.
Smile effect of the bands

1. Migration was too fast. 2. Migration was too hot (changing the pH and altering the migration). Slow down the migration or run the gel in the cold room or on ice.
Uneven band size in lanes probed for the same protein

Gel has set too quickly while casting and the acrylamide percentage is not even along the lanes. Review the recipe of the gel and the addition of TEMED to the gels, add a little 0.1% SDS in water to the top of the migrating gel while it sets to stop it from drying.
Uneven staining of the gel

1. 2. 1. 2. Contamination from bacteria Not enough antibody Keep antibodies at 4C and use fresh buffers to cover the gel. Make sure the membrane is covered with the antibody/incubate under agitation.
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Further useful western blot protocols

There are many more useful western blot procedures and guides on our protocols web pages. Please see the following URL addresses for more information: Blocking with immunizing peptide www.abcam.com/blockingwithimmunizingpeptide De-phosphorylation www.abcam.com/de-phosphorylation Histone blotting www.abcam.com/histoneblotting Histone extraction www.abcam.com/histoneextraction Mitochondrial purification www.abcam.com/mitochondrialpurification Nuclear fractionation www.abcam.com/nuclearfractionation Phospho-proteins www.abcam.com/phospho-proteins Soluble (S-100) fractionation www.abcam.com/soluble(s-100)fractionation
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Stripping for reprobing www.abcam.com/strippingforreprobing
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SECTION 6: Immunohistochemistry and Immunocyctochemistry

6.1 IHC-Paraffin protocol (IHC-P)
Immunohistochemistry (IHC) is a method for demonstrating the presence and location of proteins in tissue sections. Though less sensitive quantitatively than immunoassays such as western blotting or ELISA, it enables the observation of processes in the context of intact tissue. This is especially useful for assessing the progression and treatment of diseases such as cancer. In general, the information gained from IHC combined with microscopy literally provides a big picture that can help make sense of data obtained using other methods. Immunohistochemical staining is accomplished with antibodies that recognize the target protein. Since antibodies are highly specific, the antibody will bind only to the protein of interest in the tissue section. The antibody-antigen interaction is then visualized using either chromogenic detection, in which an enzyme conjugated to the antibody cleaves a substrate to produce a colored precipitate at the location of the protein, or fluorescent detection, in which a fluorochrome is conjugated to the antibody and can be visualized using fluorescence microscopy. IHC-P refers to the staining of tissues that have been fixed (usually in neutral buffered formalin) and then embedded in paraffin before being sectioned. The basic steps of the IHC-P protocol are as follows: 1. Fixing and embedding the tissue 2. Cutting and mounting the section 3. Deparaffinizing and rehydrating the section 4. Antigen retrieval 5. Immunohistochemical staining 6. Counterstaining (if desired) 7. Dehydrating and stabilizing with mounting medium 8. Viewing the staining under the microscope
6.1.1 Optimizing a new antibody for IHC-P

1. Antigen retrieval 2. Primary antibody concentration 3. Detection
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6.1.2 Fixation 6.1.3 Deparaffinization 6.1.4 Antigen retrieval

1. Buffer solutions for heat induced epitope retrieval 2. Heat induced epitope retrieval methods 3. Enzymatic antigen retrieval
6.1.5 Immunohistochemical staining

1. 2. 3. 4. General guidelines Protocol Controls Signal amplification
6.1.6 Resources
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Immunohistochemical staining
IHC-P IHC-Fr and ICC
Deparaffinization and dehydration Xylene, Xylene 1:1 100% ethanol, 100% ethanol down to 50 % ethanol Antigen retrieval Heat in citrate buffer pH 6 for 5 -20 min Or Enzymatic (trypsin, proteinase K)
Fix slides 4% PFA for 10 min Or Methanol (ice cold) for 10 min Or Acetone (ice cold) for 10 min
Block with 5% serum or BSA for 30 min to 1 hr
Wash with PBS 0.2% Tween 20. 4C for 5 minutes
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Permeabilize the cells if detecting an intracellular target
0.2% Triton for 10 minutes (not necessary if fixed in acetone or methanol)
Incubate with primary antibody 30 min to 2 hr RT or overnight 4C
Wash with PBS 0.2% Tween 20. 4C for 5 minutes
Key
Incubate with conjugated secondary antibody 30 min to 2 hr RT Cell
Antigen Substrate Enzymatic Detection Primary antibody Colored product Conjugated Secondary antibody
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6.1.1 Optimization of a new antibody for IHC

When using a new antibody in IHC-P, the antibody must be tested to find the optimal staining conditions. Each antigen has a preferred method of antigen retrieval, and each antibody has an optimal dilution. Antigen retrieval Try staining without antigen retrieval, and also using the following antigen retrieval methods. Detailed protocols for these procedures are in the Antigen Retrieval section 6.1.4 on page 30. 1. Heat induced: Sodium citrate 10 mM, pH 6.0 2. Heat induced: Tris/EDTA pH 9.0 3. Enzymatic: trypsin, pepsin, or other protease Once the optimal antigen retrieval method is established, the antibody concentration can be fine tuned. Primary antibody concentration If the concentration of the antibody is provided, we recommend trying 0.5 g/ml and 5 g/ml overnight at 4C. If the antibody is unpurified, we recommend starting with the following starting dilutions, and also testing a 20 fold higher dilution. 1. Whole antiserum: 1/50 2. Ascites: 1/100 3. Tissue Culture supernatant: undiluted (also referred to as neat) Detection We recommend horseradish peroxidase (HRP) for visible light microscopy. Peroxide/DAB are the substrate and recommended chromogen for horseradish peroxidase. Various fluorochrome conjugated antibodies are available for fluorescent microscopy; choice will be dictated by the needs of the experiment.
6.1.2 Fixation
Proper fixation is key for the success of immunohistochemistry. Ten percent neutral buffered formalin (NBF) is most commonly used. Where Abcams datasheets state IHC-P as a tested application, this fixative has been used unless stated otherwise. Other fixatives such as paraformaldehyde (PFA) or Bouin solution (formalin/picric acid) are used less frequently. Recipes for these fixatives can be found in the Buffers section beginning on page 77. The ideal fixation time will depend on the size of the tissue block and the type of tissue, but fixation between 18-24 hr seems to be ideal for most applications. Under fixation can lead to edge staining, with strong signal on the edges of the section and no signal in the middle; over fixation can mask the epitope. Antigen retrieval can help overcome this masking, but if the tissue has been fixed for a long period of time (i.e. over a weekend), there may be no signal even after antigen retrieval. After fixation, the tissue block is embedded in paraffin, then cut in a microtome to the desired thickness (approximately 5 to 20 microns is ideal for IHC depending on the tissue) and affixed onto the slide. Tissue sections are best mounted on positively charged or APES (amino-propyl-tri-ethoxy-silane) coated slides. Once mounted, the slides should be dried to remove any water that may be trapped under the section. This can be done by leaving the slide at room temperature overnight. If there is a problem with the section adhering to the slide, you may also incubate the slide at 60C for a few hours.
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6.1.3 Deparaffinization
Before proceeding with the staining protocol, the slides must be deparaffinized and rehydrated. Incomplete removal of paraffin can cause poor staining of the section. Materials and reagents Xylene 100% ethanol 95% ethanol Method Place the slides in a rack, and perform the following washes: 1. Xylene: 2 X 3 min 2. Xylene 1:1 with 100% ethanol: 3 min 3. 100% ethanol: 2 X 3 min 4. 95% ethanol: 3 min 5. 70 % ethanol: 3 min 6. 50 % ethanol: 3 min 7. Running cold tap water to rinse Keep the slides in the tap water until ready to perform antigen retrieval. At no time from this point onwards should the slides be allowed to dry. Drying out will cause non specific antibody binding and therefore high background staining.
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6.1.4 Antigen retrieval

Most formalin fixed tissue requires an antigen retrieval step before immunohistochemical staining can proceed. This is due to the formation of methylene bridges during fixation, which cross-link proteins and therefore mask antigenic sites. The two methods of antigen retrieval are heat mediated (also known as heat induced epitope retrieval, or HIER) and enzymatic. Both antigen retrieval methods serve to break the methylene bridges and expose the antigenic sites in order to allow the antibodies to bind. Some antigens prefer enzymatic to heat mediated antigen retrieval and vice versa. Enzymatic retrieval can sometimes damage the morphology of the section, so the concentration and treatment time need to be tested. Antigen retrieval with Tris/EDTA pH 9.0 buffer is suitable for most antigens. Sodium citrate pH 6.0 is also widely used. We can recommend reviewing the following useful website: www.nordiqc.org/Techniques/Epitope_retrieval.htm For an explanation of why Abcam recommends using Tris/EDTA pH 9.0 buffer before sodium citrate pH 6.0. Heat induced epitope retrieval is most often performed using a pressure cooker, a microwave, or a vegetable steamer. Additionally, some labs will use a water bath set to 60C and incubate the slides in retrieval solution overnight. Unless the antigen retrieval method is stated on the antibody datasheet, the optimal method for each antigen must be found experimentally. Abcam recommends testing several methods to find the retrieval that gives optimal staining. 1. Buffer solutions for heat induced epitope retrieval The following solutions are three of the more popular buffers for HIER. In the absence of advice from other researchers for a particular antibody, choice of retrieval buffer is best accomplished by experiment. 1. Sodium Citrate Buffer (10 mM Sodium Citrate, 0.05% Tween 20, pH 6.0) 2. 1 mM EDTA, adjusted to pH 8.0 3. Tris/EDTA Buffer (10mM Tris Base, 1 mM EDTA Solution, 0.05% Tween 20, pH 9.0)
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2. Heat induced epitope retrieval methods a) Pressure cooker Slides should be placed in a metal rack for this procedure. Materials and reagents Domestic stainless steel pressure cooker Hot plate Vessel with slide rack to hold approximately 400-500 ml Antigen retrieval buffer (i.e. Tris/EDTA pH 9.0, sodium citrate pH 6.0) Method 1. Add the appropriate antigen retrieval buffer to the pressure cooker. Place the pressure cooker on the hotplate and turn it on full power. Do not secure the lid of the pressure cooker at this point, simply rest it on top. While waiting for the pressure cooker to come to a boil, deparaffinize and rehydrate the sections as described above. 2. Once boiling, transfer the slides from the tap water to the pressure cooker. USE CARE WITH HOT SOLUTION - USE FORCEPS! Secure the pressure cooker lid as in the manufacturers instructions. 3. As soon as the cooker has reached full pressure (see the manufacturers instructions), time 3 min (See note 1). 4. When 3 min has elapsed, turn off the hotplate and place the pressure cooker in an empty sink. 5. Activate the pressure release valve (see the manufacturers instructions) and run cold water over the cooker. Once de-pressurized, open the lid and run cold water into the cooker for 10 min. USE CARE WITH HOT SOLUTION! (See note 2). 6. Continue with the immunohistochemical staining protocol. Notes: 1. Three min is only suggested as a starting point antigen retrieval time. Less than 3 min may leave the antigens under retrieved, leading to weak staining. More than 3 min may leave them over retrieved, leading to non specific background staining and also increasing the chances of sections dissociating from the slides. A control experiment is recommended beforehand, where slides of the same tissue section are retrieved for 1, 2, 3, 4 and 5 min before being immunohistochemically stained to evaluate optimum antigen retrieval time for the particular antibody being used. 2. This is to allow the slides to cool enough so they may be handled, and to allow the antigenic site to re-form after being exposed to such high temperature
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b) Microwave The use of a domestic microwave is inadvisable. Hot and cold spots are common, leading to uneven antigen retrieval. Antigen retrieval times are usually longer, due to the absence of a pressurized environment, nearly always leading to section dissociation. A scientific microwave is much more appropriate. Most brands have on board pressurized vessels and can keep the temperature at a constant 98C to avoid section dissociation. The only drawback is the expense of purchasing one! When using this method, it is possible for the buffer to boil over, and a large amount of the retrieval buffer will evaporate. Be sure to watch the buffer level of the slide vessel, and add more buffer if necessary. Do not allow the slides to dry out.
Slides should be placed in a plastic rack and vessel for this procedure. Standard glass histologystaining racks and vessels will crack when heated.
Materials and reagents Domestic (850W) or scientific microwave Microwaveable vessel with slide rack to hold approximately 400-500 ml or Coplin jar Antigen retrieval buffer (e.g. Tris/EDTA pH 9.0, sodium citrate pH 6.0, etc.) Method 1. Deparaffinize and rehydrate the sections as described above. 2. Add the appropriate antigen retrieval buffer to the microwaveable vessel (See note i). 3. Remove the slides from the tap water and place them in the microwaveable vessel. Place the vessel inside the microwave. If using a domestic microwave, set to full power and wait until the solution comes to the boil. Boil for 20 min from this point. If using a scientific microwave, program so that antigens are retrieved for 20 min once the temperature has reached 98C. (See note ii). 4. When 20 min has elapsed, remove the vessel and run cold tap water into it for 10 min. USE CARE WITH HOT SOLUTION! (See note iii). 5. Continue with the immunohistochemical staining protocol. Notes i. Use a sufficient volume of antigen retrieval solution in order to cover the slides by at least a few centimeters if using a non sealed vessel to allow for evaporation during the boil. Be sure to watch for evaporation and for boiling over during the procedure, and do not allow the slides to dry out! ii. Twenty min is only a suggested antigen retrieval time. Less than 20 min may leave the antigens under retrieved, leading to weak staining. More than 20 min may leave them over retrieved, leading to non specific background staining and also increasing the chances of sections dissociating from the slides. A control experiment is recommended beforehand, where slides of the same tissue section are retrieved for 5, 10, 15, 20, 25 and 30 min before being immunohistochemically stained to evaluate optimum antigen retrieval time for the particular antibody being used. iii. This allows the slides to cool enough so they may be handled, and allows the antigenic site to re-form after being exposed to high temperature. c) Vegetable steamer Many labs use a vegetable steamer or rice cooker for heat mediated antigen retrieval. The procedure is similar to microwaving in that it maintains the temperature of the buffer at 100C, but without the vigorous boiling of the microwave method. This method may be adapted to a water bath set at 100C in place of the steamer.
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Slides should be placed in a plastic or metal rack and vessel for this procedure. Standard glass histology staining racks and vessels will crack when heated.
Materials and reagents Vegetable steamer Vessel with slide rack to hold approximately 400-500 ml (or 250 ml if using Tissue Tek containers) Antigen retrieval buffer (e.g. Tris/EDTA pH 9.0, sodium citrate pH 6.0, etc.)
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Method 1. Deparaffinize and rehydrate the sections as described above. 2. Set up the vegetable steamer according to the manufacturers instructions and preheat. 3. Preheat the appropriate antigen retrieval buffer to boiling in a flask (a microwave is handy for this). 4. Put the container that will hold the rack of slides into the vegetable steamer. 5. Carefully add the hot buffer to the container, followed by the rack of slides. If more convenient, add the buffer to the container before placing the container in the steamer. 6. Close the lid of the steamer. The container of buffer should also have a lid. The rack of slides will initially bring the temperature of the antigen retrieval solution down but it will return to 95-100C within several min. 7. Keep the container in the steamer for 20 min from this point. (See note ii for the microwave method). 8. When 20 min has elapsed, remove the vessel and run cold tap water into it for 10 min. USE CARE WITH HOT SOLUTION! (See note iii for the microwave method). 9. Continue with the immunohistochemical staining protocol. 3. Enzymatic antigen retrieval Choice of enzyme will be indicated on the datasheet for the antibody. If not, trypsin has been shown to be useful for a wide range of antigens that require retrieval post formalin/PFA fixation. There are at least two methods for applying the enzyme solution to the tissue: directly pipetting the solution onto the tissue on the slide, or placing a rack of tissue slides into a container of enzyme solution. The first method uses less reagent, but since each slide needs to be handled individually, the incubation time needs to be monitored carefully to ensure all slides are receiving the same treatment. For this reason, it is easier to treat large batches of slides (e.g. > 5) by immersing them in a container of enzyme solution. If using an automated staining system (e.g. Ventana), consult the manufacturer for an appropriate enzymatic retrieval protocol. a) Pipetting method Materials and reagents 37C incubator Humidified chamber (either the incubator itself or a container with a wet paper towel) Two slide rack containers of TBS (See Buffers section beginning on page 77 for TBS recipe.) Enzymatic antigen retrieval solution (For trypsin, see below. For pepsin and proteinase K, see Buffers section beginning on page #). The following method uses trypsin. There are commercially available trypsin preparations optimized for IHC (Abcam has a convenient trypsin product, catalogue ID ab970), or it can be prepared as described in the Buffers section 11 beginning on page 77. Method 1. Prepare the trypsin and preheat to 37C. Carefully blot excess water from around the tissue section and pipette the enzyme solution (generally 50-100 l will suffice) onto the section. It may be necessary to spread the solution around the section with the pipette tip; be careful not to damage the tissue. 2. Place the slides in a humidified container and then into the 37C incubator. Avoid placing the slides directly on the incubator shelves as there will be variations in temperature that could affect staining intensity. Ideally, the container holding the slides is pre heated in the incubator. 3. After 10-20 min (this will need to be optimized), remove the slides from the incubator and transfer to a rack in a container of tap water. Rinse by running tap water for 3 min. 4. Continue with the immunohistochemical staining protocol. b) Immersion method Materials and reagents 37C water bath Slide racks and slide rack containers Enzymatic antigen retrieval solution (For trypsin, see pipetting method. For pepsin and proteinase K, see Buffers section beginning on page 77).
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Method 1. Set water bath to the optimal temperature for the enzyme you are using. Add ultrapure water to two containers that can hold slide racks. Place the containers into the water bath to warm. (See note ii). 2. Deparaffinize and rehydrate sections described as above. Place slides in one water container to warm (See note iii). 3. Prepare the enzymatic antigen retrieval buffer from the warm water in the other container, and then return the container to the water bath to allow the solution to reheat (See note iv). 4. Transfer the warmed slides into the enzyme solution for 10-20 min (See note v) with intermittent gentle agitation, then remove the slides and place them in running tap water for 3 min to rinse off the enzyme. 5. Continue with the immunohistochemical staining protocol. Notes i. Be sure to read the manufacturers literature for the enzyme you choose, as some enzymes require specific buffers and cofactors for activity. ii. Use a sufficient volume of water or buffer to cover the slides. iii. Placing cold slides into the enzyme solution will lower the temperature of the solution, reducing enzyme activity and leading to under retrieval of the antigenic site. iv. Prepare the enzymatic antigen retrieval solution as quickly as possible to avoid impairing the activity of the enzyme. Allow this solution to return to required temperature before introducing the slides. v. 10 to 20 min is only suggested as a starting point incubation time. Less than 10 min may leave the antigens under retrieved, leading to weak staining. More than 20 min may leave them over retrieved, leading to non specific background staining and also increasing the chances of sections dissociating from the slides or damage to the morphology of the tissue. A control experiment is recommended beforehand, where slides of the same tissue section are incubated in the enzyme solution for 10, 15, 20, 25, and 30 min before being immunohistochemically stained to evaluate optimum antigen retrieval time for the particular antibody being used.
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6.1.5 Immunohistochemical staining

1. General guidelines The following protocol assumes the laboratory does not have an automated stainer or other capillary gap system that allows rapid application and rinsing of reagents (e.g. Shandon Sequenza). Reagents can be applied manually by pipette or protocol can be adapted to automated and semi automated systems if these are available. All incubations should be carried out in a humidified chamber to avoid drying of the tissue. Drying at any stage will lead to non specific binding and ultimately high background staining. A shallow, plastic box with a sealed lid and wet tissue paper in the bottom is an adequate chamber, as long as the slides are kept off the paper and can lay flat so that the reagents dont drain off! A good solution is to cut a plastic serological pipette into lengths to fit your incubation chamber. Glue them in pairs to the bottom of the chamber, with the 2 individual pipette tubes of each pair being placed about 4 cm apart. This provides a level and raised surface for the slides to rest on away from the wet tissue paper. Dilutions of the primary and secondary antibody are listed on the datasheets or are determined by testing a range. Adjust dilutions appropriately from the results obtained. Adhere strictly to all incubation times in the protocol. For enzymatic methods, horseradish peroxidase (HRP) or alkaline phosphatase (AP) are the most commonly used enzymes. There are a number of chromogens used with these enzymes. 2. Protocol Please refer to Buffers section 11 beginning on page 77 for recipes. If necessary, perform antigen retrieval before commencing with the following protocols. Day 1 1. If using an HRP conjugate for detection, blocking of endogenous peroxidase can be performed here but we recommend waiting until after the primary antibody incubation. 2. Wash the slides 2 X 5 min in TBS plus 0.025% Triton X-100 with gentle agitation. 3. Block in 10% normal serum with 1% BSA in TBS for 2 hr at room temperature. Drain slides for a few seconds (do not rinse) and wipe around the sections with tissue paper. 4. Apply primary antibody diluted in TBS with 1% BSA. 5. Incubate overnight at 4C.
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Day 2 1. Rinse 2 X 5 min in TBS 0.025% Triton X-100 with gentle agitation. 2. If using an HRP conjugate for detection, incubate the slides in 0.3% H2O2 in TBS for 15 min to block endogenous peroxidase. 3. For enzymatic detection (HRP or AP secondary conjugates): Apply enzyme conjugated secondary antibody to the slide diluted to the concentration recommended by the manufacturer in TBS with 1% BSA, and incubate for 1 hr at room temperature. For fluorescent detection: Apply fluorochrome conjugated secondary antibody to the slide diluted to the concentration recommended by the manufacturer in TBS with 1% BSA, and incubate for 1 hr at room temperature.
This step should be done in the dark to avoid photobleaching.
4. Rinse 3 X 5 min in TBS. If using fluorescent detection, end at this step and use a mounting medium to mount the tissue with a cover slip. If visualizing the protein with a chromogen, continue with the following steps. 5. Develop with chromogen for 10 min at room temperature. 6. Rinse in running tap water for 5 min.
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7. Counter stain (if required). 8. Dehydrate, clear and mount. 3. Controls To estimate the contribution of the non specific interaction and Fc receptor binding, staining protocols using an antibody directed to an irrelevant antigen (e.g. BrdU) having the same isotype as the antibody of interest may be analyzed in parallel with the antibody of interest. The antibody directed to the irrelevant antigen is known as the isotype control. For whole serum antibodies, use normal serum from a non immunized animal of the same species as the primary antibody. If an isotype control is not available, a negative antibody control is recommended. Simply replace the primary antibody with antibody diluent. A positive tissue control is strongly recommended to ensure that the antibody is performing as expected. Depending on the experiment, it may also be useful to include a negative tissue control; a tissue in which the protein of interest is not expected to be found. Notes:
The use of 0.025% Triton X-100 in the TBS helps reduce surface tension, allowing reagents to cover the whole tissue section with ease. It is also believed to dissolve Fc receptors, therefore reducing non specific binding. Abcam recommends TBS to give a cleaner background than PBS.
1. The secondary antibody may cross react with endogenous immunoglobulins in the tissue. This is minimized by pre-treating the tissue with normal serum from the species in which the secondary was raised. The use of normal serum before the application of the primary antibody also eliminates Fc receptor binding of both the primary and secondary antibodies. BSA is included in the antibody dilution buffer to reduce non specific binding caused by hydrophobic interactions. If the tissue samples are fixed with an aldehyde fixative such as formalin, paraformaldehyde or glutaraldehyde and immunofluorescence (IF) is the detection method, consider including 0.3 M glycine in the blocking buffer before applying the primary antibody. Glycine will bind free aldehyde groups that would otherwise bind the primary and secondary antibodies and lead to high background. Background staining due to free aldehyde groups is more likely to occur when the fixative is glutaraldehyde or paraformaldehyde. 2. The primary antibody should be diluted to the manufacturers recommendations or to a previously optimized dilution. If there is no suggested starting point, we recommend following the recommendations. Most antibodies will be used in IHC-P at a concentration between 0.5 and 10 g/ml. Make sure the primary antibody is raised in a species different from the tissue being stained. If, for example, you had mouse tissue and your primary antibody was raised in a mouse, an anti-mouse IgG secondary antibody would bind to all the endogenous IgG in the mouse tissue, leading to high background. Use of mouse monoclonals on mouse tissue is discussed in our mouse-on-mouse protocol.
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3. Overnight incubation allows antibodies of lower affinity more time to bind to the antigen. However, regardless of the antibodys affinity for its target, once the binding has reached saturation point or equilibrium, no more binding can take place. Overnight incubation ensures that binding reaches equilibrium. 4. Peroxide (H2O2) suppresses endogenous peroxidase activity and therefore reduces background staining. To check for the presence of endogenous peroxidases, incubate a tissue slide after re-hydration in a solution of DAB (3,3 Diaminobenzidine substrate). If areas of the section appear brown under the microscope, peroxidase is present, and a blocking step should be included. Some epitopes are modified by peroxide, leading to reduced antibody:antigen binding. Incubating sections with peroxide after the primary incubation avoids this problem. Peroxide can be diluted in TBS or water. Some laboratories use methanol which is useful for blood smears or other peroxidase rich tissues such as liver. Peroxide diluted in methanol tends to reduce damage to the tissue caused by the reaction in aqueous solutions. For other tissue though, we recommend diluting in TBS or water. Reduced binding of some antibody:antigen pairs, in particular cell surface proteins, has been observed after methanol/peroxide incubation. Blocking of endogenous peroxidases is only required for peroxidase conjugates such as HRP. 5. Develop the colored product of the enzyme with the appropriate chromogen. The choice depends on which enzyme label you are using, the colored end product you prefer and whether you are using aqueous or organic mounting media. Some commonly used substrates are listed below:
Enzyme
Substrate
Color
Advantages
Disadvantages
Abcam ID
3,3-Diaminobenzidine Brown (DAB) Horseradish peroxidase (HRP) 3-Amino-9-ethyl carbazol (AEC) Red
Intense color; permanent
ab675 Endogenous peroxidase activity in the tissue can lead to false positive staining. AEC is alcohol soluble and incompatible with organic mounting media.
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Intense color; contrasts well with blue for double staining
Alkaline phosphatase (AP)
5-bromo-4-chloro-3indoyl phosphate; Nitroblue tetrazolium (BCIP/NBT)
Blue
Intense color Endogenous alkaline phosphatase activity in the tissue can lead to false positive staining.
ab7413 ab7468
Vector Blue
Blue
Less intense color, but better for double staining
Glucose oxidase
Nitroblue tetrazolium (NBT)
Blue
No endogenous enzyme activity
Low staining intensity (high concentration of primary and secondary antibodies required for effectiveness)
6. Some commonly used counterstains to observe tissue and cell morphology are hematoxylin (blue), nuclear fast red, or methyl green. When using fluorescent detection, DAPI (blue) or propidium iodide/PI (red) can be used to counterstain. 7. Dont forget that DAB is a suspected carcinogen. Wear the appropriate protective clothing. Deactivate it with sodium hypochlorite in a sealed container overnight (reaction it produces noxious fumes) and dispose of it according to laboratory guidelines. If using AP, add 0.24 mg/ml Levamisole to the chromogen solution. Levamisole suppresses endogenous phosphatase activity and therefore reduces background staining. 8. If using AEC, Fast Red, INT or any other aqueous chromogen then dont forget that they are alcohol soluble. Use a suitable aqueous mounting media. Dont dehydrate and clear as in step 9!
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9. Dehydrate and clear DAB, New Fuchsin, Vega Red, NBT, TNBT or any other organic chromogen developed sections by sending them through the rehydration protocol listed in the opposite order. 1. 2. 3. 4. 5. 6. Place slides in 50% ethanol 3 min, 70% ethanol 3 min. 95% ethanol 3 min. 100% ethanol 3 min. Xylene 1:1 with 100% ethanol 3 min. Xylene 2 X 3 min.
Mount sections in a suitable organic mounting media. Sections mounted in organic mounting media have a better refractive index than those mounted in aqueous mounting media. This means that the image seen under the microscope will be sharper and clearer. 4. Signal amplification To achieve a stronger signal, various strategies have been developed to add more enzyme or fluorochrome to the target of interest. a) Avidin-biotin complex (ABC) This technique, developed by Su-Ming Hsu and colleagues (J Histochem Cytochem. 1981 Apr 29 (4):577-80), utilizes the high affinity of avidin, a protein found in chicken egg white, for biotin, an enzyme co-factor in carboxylation reactions. Avidin has four binding sites for biotin and binding is essentially irreversible. In brief, the primary antibody is bound to the protein of interest. A biotinylated secondary antibody is then bound to the primary antibody. In a separate reaction, a complex of avidin and biotinylated enzyme is formed by mixing the two in a ratio that leaves some of the binding sites on avidin unoccupied. This complex is then incubated with the tissue section after the antibody incubations. The unoccupied biotin binding sites on the complex bind to the biotinylated secondary antibody. The result is more enzyme attached to the target than is possible using an enzyme conjugated secondary or primary antibody.
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The components of the avidin-biotin complex are commercially available in kits that provide the two reagents and instructions for combining them in the optimal ratio. The complex can be used with any of Abcams biotinylated antibodies. One concern is the presence of endogenous biotin in tissues such as kidney, liver, brain, prostate, colon, intestines, and testes, which can bind the avidin-biotin complex leading to background staining. (Wang and Pevsner, Cell Tissue Res. 1999 Jun;296(3):511-6.) To block binding to endogenous biotin, Abcam offers a blocking kit, ab3387. b) Labeled streptavidin biotin (LSAB) This method is similar to ABC in that it utilizes the interaction of streptavidin (similar to avidin in binding affinity) and biotin. The primary antibody is followed by a biotinylated anti-Ig secondary antibody, followed by streptavidin conjugated to an enzyme or fluorochrome. Abcam offers a streptavidin HRP conjugate, ab7403. Streptavidin produces less non specific background staining than avidin since it is non glycosylated (unlike avidin). Consequently, it does not interact with lectins or other carbohydrate binding proteins. LSAB was shown to be 4 to 8 times more sensitive than ABC in the following publication: see Giorno R, Diagno Immunol. 1984;2(3):161-6. c) HRP polymer Both avidin-biotin methods (ABC and LSAB) are losing favor to new polymer-enzyme-antibody products that consist of a secondary antibody (e.g. anti-mouse and/or rabbit IgG) attached to a polymer-enzyme complex. One step is eliminated compared to the avidin-biotin methods and the issue of endogenous biotin is avoided. Abcam offers a goat anti-rabbit/mouse IgG HRP polymer, ab2891. d) Tyramide signal enhancing (TSE) One of the most effective amplification procedures is the patented and licensed method, TSE (also known as TSA or CSA, depending on the manufacturer of the commercially available kits). It is particularly useful for detection of relatively sparse antigens that other systems have difficulty detecting, and for improving results obtained with poorly performing antibodies. The method relies on a peroxidase catalyzed reaction to covalently attach the tyramide portion of tyramine-protein conjugates to the antibody, after first applying a primary antibody and secondary HRP conjugate. The covalently attached protein cannot be washed off, even if the slides are treated to remove the antibodies, since the tyramide bond is covalent. To obtain a signal, an antibody enzyme or fluorochrome conjugate is directed against the protein portion of the tyramine protein conjugate. In one commercially available version of the method, the protein is biotin and a streptavidin enzyme conjugate is applied instead of an antibody conjugate. The disadvantages of the procedure are the expense of the kits and the time required to perform the multiple steps.
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6.1.5 Resources
IHC World (www.ihcworld.com) has a wealth of information on antigen retrieval, positive controls, and trouble shooting the immunohistochemical procedure. Histonet (www.histosearch.com/histonet.html) searches archived messages posted to the Histonet list server from scientists around the world. Nordic immunohistochemical Quality Control (www.nordiqc.org) has information regarding appropriate positive controls and antigen retrieval steps for many target proteins.
6.2 Immunohistochemistry (IHC-Fr)-Frozen sections protocol

Frozen sections: Once mounted on APES coated slides, frozen sections are best kept at -80C until needed. 1. When required, leave to warm at room temperature for 5 min. 2. Pre-cool the fixative (acetone, methanol or ethanol) at -20C for 30 min. (Abcam recommends starting with acetone) 3. Fix with the pre cooled fixative for 5-10 min, at room temperature. 4. Rinse 3-4 X in PBS. 5. Continue with the immunohistochemical staining protocol. The absence of a formaldehyde based fixative eliminates the need for an antigen retrieval step. However, if frozen tissue or cytological specimens have been fixed in formalin, antigen retrieval can be attempted, although the friable nature of the specimens, in particular brain tissue, may compromise the success. The following reference describes a protocol in which slides are treated with 3-aminopropyltriethoxysilane (APES) before placing sections on the slides. This treatment improved adhesion, allowing heat mediated antigen retrieval with minimal damage to the tissue morphology:
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Warembourg M, Leroy D., Microwave pre treatment of sections to improve the immunocytochemical detection of progesterone receptors in the guinea pig hypothalamus. J Neurosci Methods. 2000 Dec 15;104(1):27-34. A more thorough discussion of antigen retrieval applied to frozen tissue sections is found in the following reference: Yamashita S, Okada Y. Application of heat induced antigen retrieval to aldehyde fixed fresh frozen sections. J Histochem Cytochem. 2005 Nov;53(11):1421-32.
If the tissue samples are fixed with an aldehyde fixative such as formalin, paraformaldehyde or glutaraldehyde and immunofluorescence (IF) is the detection method, consider including 0.3 M glycine in the blocking buffer, before applying the primary antibody. Glycine will bind free aldehyde groups that would otherwise bind the primary and secondary antibodies, leading to high background. Background due to free aldehyde groups is more likely to occur when the fixative is glutaraldehyde or paraformaldehyde. See IHC-Paraffin protocol (IHC-P) for detailed protocols for chromogenic and fluorescent detection.
6.3 Immunocytochemistry (ICC) protocol

General procedure: 1. Coat coverslips with polyethylineimine or poly-L-lysine for 1 hr at room temperature. 2. Rinse coverslips well with sterile H2O (3 X 5 min each). 3. Allow coverslips to dry completely and sterilize them under UV light for at least 4 hr. 4. Grow cells on glass coverslips or prepare cytospin or smear preparation. 5. Rinse briefly in phosphate buffered saline (PBS). Fixation: 1. Fix the samples either in ice cold methanol, acetone (1-10 min). Or fix in 3-4% paraformaldehyde in PBS pH 7.4 for 15 min at room temperature. 2. Wash the samples twice with ice cold PBS.
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Permeabilization: If the target protein is expressed intracellularly, it is very important to permeabilize the cells. Note: acetone fixed samples do not require permeabilization. 3. Incubate the samples for 10 min in PBS containing 0.25% Triton X-100 (or 100 M digitonin or 0.5% saponin). Triton X-100 is the most popular detergent for improving the penetration of the antibody. However, it is not appropriate for the use of membrane associated antigens since it destroys membranes. 4. Wash cells in PBS 3 X 5 min. Blocking and incubation: 5. Incubate cells with 1% BSA in PBST for 30 min to block unspecific binding of the antibodies (alternative blocking solutions are 1% gelatin or 10% serum from the species in which the secondary antibody was raised).
If the tissue samples are fixed with an aldehyde fixative such as formalin, paraformaldehyde or glutaraldehyde and immunofluorescence (IF) is the detection method, consider including 0.3 M glycine in the blocking buffer. Glycine will bind free aldehyde groups that would otherwise bind the primary and secondary antibodies, leading to high background. Background staining due to free aldehyde groups is more likely to occur when the fixative is glutaraldehyde or paraformaldehyde.
6. Incubate cells with the antibody (diluted in 1% BSA in PBST) in a humidified chamber for 1 hr at room temperature or overnight at 4C. 7. Decant the solution and wash the cells with PBS 3 X 5 min. 8. Incubate cells with the secondary antibody in 1% BSA for 1 hr at room temperature in the dark.
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9. Decant the secondary antibody solution and wash with PBS 3 X 5 min in the dark. Counter staining: 10. Incubate cells with 0.1-1 g/ml Hoechst or DAPI (DNA stain) for 1 min. 11. Rinse with PBS. Mounting: 12. Mount coverslip with a drop of mounting medium. 13. Seal coverslip with nail polish to prevent drying and movement under microscope. 14. Store in the dark at -20C or +4C.
6.4 Fixation and permeabilization in IHC/ICC

Fixation: Fixation should immobilize antigens while retaining cellular and subcellular structure. It should also allow for access of antibodies to all cells and subcellular compartments. The fixation and permeabilization method used will depend on the sensitivity of the epitope and the antibodies themselves, and may require some optimization. Fixation can be done using crosslinking reagents, such as paraformaldehyde. These are better at preserving cell structure, but may reduce the antigenicity of some cell components as the crosslinking can obstruct antibody binding. For this reason, antigen retrieval techniques may be required, particularly if there is a long fixation incubation or if a high percentage of crosslinking fixative is used. Another option is to use organic solvents. These remove lipids while dehydrating the cells. They also precipitate proteins on the cellular architecture. 1. 4% Paraformaldehyde Add 4% paraformaldehye to slides for 10 min only. Wash with PBS or PBS with 1% BSA.
Note: Fixing in paraformaldehyde for more than 10-15 min will cross link the proteins to the point where antigen retrieval may be required to ensure the antibody has free access to bind and detect the protein.
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2. Ethanol Add 100-200 l per slide of cooled 95% ethanol, 5% glacial acetic acid for 5-10 min. Wash with PBS or PBS with 1% BSA. 3. Methanol Add 100-200 l per slide of ice cold methanol. Place at -20C for 10 min. Wash with PBS or PBS with 1% BSA.
Note: Methanol will also permeabilize. Some epitopes are very sensitive to methanol as it can disrupt epitope structure. Can try acetone instead for permeabilization if required.
4. Acetone Add 100-200 l per slide ice cold acetone. Place at -20C for 5 to 10 min. Wash with PBS or PBS with 1% BSA.
Note: acetone will also permeabilize. Consequently, no further permeabilization step is required.
Permeabilization: Permeabilization is only required when the antibody needs access to the inside of the cells to detect the protein. These include intracellular proteins and transmembrane proteins whose epitopes are in the cytoplasmic region. Solvents: 1. Acetone fixation will also permeabilize 2. Methanol fixation can be used to permeablize but is not always suitable. These reagents can be used to fix and permeabilize, or can be used after fixation with a crosslinking agent such as paraformaldehyde. Detergents: 1. Triton or NP-40 Use 0.1 to 0.2% in PBS for 10 min only. These will also partially dissolve the nuclear membrane and are therefore very suitable for nuclear antigen staining.
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Note: as these are harsh detergents, they will disrupt proteins when used at higher concentrations or for longer amounts of time, affecting staining results.
2. Tween 20, Saponin, Digitonin and Leucoperm Use 0.2 to 0.5% for 10 to 30 min. These are much milder membrane solubilizers. They will give large enough pores for antibodies to go through without dissolving the plasma membrane. They are suitable for antigens in the cytoplasm or the cytoplasmic face of the plasma membrane and for soluble nuclear antigens. Special recommendations: Cytoskeletal, viral and some enzyme antigens usually give optimal results when fixed with acetone, ethanol or formaldehyde (high concentration). Antigens in cytoplasmic organelles and granules will require a fixation and permeabilization method depending on the antigen. The epitope needs to remain accessible.
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6.5 Perfusion fixation

For many purposes, adequate fixation is obtained by simple immersion of small tissue pieces into the fixative solution, and this is the only mode of fixation possible for many tissues. However, a more rapid and uniform fixation is usually obtained if the fixative solution is perfused via the vascular system, either through the heart or through the abdominal aorta. The following procedures provide fixation of most rat organs with 4% paraformaldehyde. Materials Anaesthetic Scissors, forceps, and clamps for surgical procedures Small forceps with fine claws Scalpel Vials (5-10 ml) with lids for specimens 0.9% saline 500 ml beakers 4% paraformaldehyde, fixation solution Gloves, eye goggles Perfusion pump (or flask with fixative placed upside down about 150 cm above the operating table) Short syringe needle for heart perfusion of aorta, length about 50 mm, outer diameter 1.3-1.5 mm Perfusion set with drip chamber as used for intravenous blood infusions 1. Perfusion fixation through the heart 1. Set up the perfusion pump; attach perfusion set and perfusion needle. First, run about 100 ml of normal tap water through the tubing to remove any residue. Then place open end of perfusion tube in a beaker filled with cold 4% paraformaldehyde (in ice box). The volume of solution should be scaled to the size of the animal, although 200-300 ml will usually be sufficient for one animal. Open valve and adjust to a slow steady drip (20 ml/min), and then close valve. 2. Set up surgery site with scissors, forceps and clamps. Give an appropriate amount of anesthetic to the animal. Once the animal is under anesthesia, place it on the operating table with its back down. You may use some tape to hold the appendages so that the animal is securely fixed. 3. Use pinch response method to determine depth of anesthesia. Animal must be unresponsive before proceeding with the following steps. 4. Make an incision with scalpel through the abdomen the length of the diaphragm. With sharp scissors, cut through the connective tissue at the bottom of the diaphragm to allow access to the rib cage. 5. With large scissors, blunt side down, cut through ribs just left of the rib cage midline. 6. Make one center or two end horizontal cuts through the rib cage, and open the thoracic cavity. Clamp open to expose heart and provide drainage for blood and fluids. 7. While holding the heart steady with forceps (it should still be beating), insert the needle directly into the protrusion of the left ventricle and extend straight up about 5 mm. Be careful not to extend the needle too far in, as it can pierce an interior wall and compromise circulation of solutions! Secure the needle by clamping in place near the point of entry. Release the valve to allow slow, steady flow of around 20 ml/min of 0.9% saline solution. 8. Make a cut in the atrium with sharp scissors, and make sure solution is flowing freely. If fluid is not flowing freely or is coming from the animals nostrils or mouth, reposition the needle. 9. When the blood has been cleared from body, change to 4% paraformaldehyde solution (200-300 ml).
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Take care not to introduce air bubbles while transferring from one solution to the other. It is best to wear protective eye goggles during the whole perfusion process, as sometimes the connecting tubes might come undone and spurt fixation solution into your eyes!
Perfusion is almost complete when spontaneous movement (formalin dance) and lightened color of the liver are observed. (Note: In general, an adult rat will require around 30-60 min of perfusion time, but this may vary depending on the size of the animal and technique.) 10. Stop the perfusion and excise the tissues of interest. Place them in vials containing the same fixation solution and fix for another 2 hr on ice or at 4C before proceeding to dehydration and embedding. For better results, immersion fix overnight at 4C.
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2. Perfusion fixation through the abdominal aorta 1. Prepare materials and animal as stated above (steps 1-3). 2. Open the abdominal cavity by a long midline incision with lateral extension, and move the intestines gently to the left side of the animal. 3. Carefully expose the aorta below the origin of the renal arteries and very gently free the aorta from overlaying adipose and connective tissues. 4. Hold the wall of the aorta firmly with fine forceps with claws about 0.5-1.0 cm from its distal bifurcation. Insert a bent needle close to the forceps towards the heart into the lumen of the aorta. 5. In very rapid succession: a) Cut a hole in the inferior vena cava with fine scissors. b) Start the perfusion. c) Clamp the aorta below the diaphragm, but above the origin of the renal arteries.
When performing these manipulations, accuracy and speed are essential and the fixation procedure is preferably carried out by two persons. It is particularly important to clamp the aorta rapidly after the perfusion has been started. This is most easily done by compressing the aorta toward the posterior wall of the peritoneal cavity with a finger (wear gloves) which is then replaced by a clamp. Finally, cut the aorta above the compression.
6. The kidney surface must blanch immediately and show a uniform, pale color. The flow rate should be at least 60-100 ml/min for an adult rat. Perfuse for 3 min. Stop the perfusion and excise and trim the tissues. Place the tissues in vials and fix in the same fixative (post fixation step) for 2 hr on ice or at 4C. For better results, immersion fix overnight at 4C. 7. The tissue is now ready for dehydration and embedding.
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6.6 Mouse on mouse staining

Staining of mouse tissue using mouse antibody is a complicated process as high levels of background are often observed. It is notoriously difficult to eliminate this background. Much of the background is caused by secondary antibody binding to endogenous mouse IgG in the tissue being stained, and to Fc receptors on B cells, plasma cells and macrophages. Abcam is unable to guarantee monoclonal mouse antibodies on mouse tissue (unless stated on the datasheet). However, there are a few tips to try and reduce this background should mouse on mouse staining be necessary: 1. Blocking of endogenous IgG: 1. Prepare tissue sections as usual. 2. At the usual blocking step, block with serum (from same species as the secondary antibody) for 30 min at room temperature. 3. Wash 3 X 2 min with PBS Tween 20. 4. Incubate sections with an unconjugated AffiniPure Fab fragment Anti-Mouse IgG (H+L) for 1 hr at room temperature, or overnight 4C. Try this blocking antibody at 0.1 mg/ml although the optimal concentration will need to be assessed by the end user. 5. Proceed with antibody staining. 2. Blocking endogenous Fc receptors: There are kits available for this which use F(ab) monomeric secondary antibodies. Other tips that can be used to decrease general background: 1. Incubate sections with 1% Triton (in PBS) at room temperature for 30 min to clean the tissue. 2. Use TBSTween 20 as a washing buffer. This often gives less background than using PBS Tween 20.
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6.7 Troubleshooting tips IHC/ICC No staining

The primary antibody and the secondary antibody are not compatible. Use a secondary antibody that was raised against the species in which the primary was raised (e.g primary is raised in rabbit, use antirabbit secondary). Not enough primary antibody is bound to the protein of interest. Use less dilute antibody. Incubate longer (e.g. overnight) at 4C. The antibody may not be suitable for IHC procedures which reveal the protein in its native (3D form). Test the antibody in a native (non denatured) WB to make sure it is not damaged. The primary/secondary antibody/amplification kit may have lost its activity due to improper storage, improper dilution or extensive freezing/thawing. Run positive controls to ensure that the primary/secondary antibody is working properly. The protein is not present in the tissue of interest. Run a positive control recommended by the supplier of the antibody. The protein of interest is not abundantly present in the tissue. Use an amplification step to maximize the signal. The secondary antibody was not stored in the dark. Always prevent the secondary antibody from exposure to light. Deparaffinization may be insufficient. Deparaffinize sections longer, change the xylene. Fixation procedures (using formalin and paraformaldehyde fixatives) may be modifying the epitope the antibody recognizes. Use antigen retrieval methods to unmask the epitope. Fix for less time. The protein is located in the nucleus (Nuclear protein) and the antibody cannot penetrate the nucleus. Add a permeabilizing agent to the blocking buffer and antibody dilution buffer. The PBS buffer is contaminated with bacteria that damage the phosphate groups on the protein of interest. Add 0.01% azide to the PBS antibody storage buffer or use fresh sterile PBS.
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High background
Blocking of non specific binding might be absent or insufficient. Increase the blocking incubation period and consider changing the blocking agent. Abcam recommends blocking with 10% normal serum for 1 hr for sections or with 1-5% BSA for 30 min for cells in culture. The primary antibody concentration may be too high. Titrate the antibody to the optimal concentration, incubate for longer but in more dilute antibody (a slow but targeted binding is best). Incubation temperature may be too high. Incubate sections or cells at 4C. The secondary antibody may be binding non specifically (damaged). Run a secondary control without primary antibody. Tissue not washed enough, fixative still present. Wash extensively with PBS between all steps. Endogenous peroxidases are active. Use enzyme inhibitors i.e. Levamisol (2 mM) for alkaline phosphatase or H2O2 (0.3% v/v) for peroxidase. (See IHC protocol). Fixation procedures (using formalin and paraformaldehyde fixatives) are too strong and modified the epitope the antibody recognizes. Change antigen retrieval method, decrease the incubation time with the antigen unmasking solution. Too much amplification (Amplification technique). Reduce amplification incubation time and dilute the amplification kit.
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Too much substrate was applied (enzymatic detection). Reduce substrate incubation time. The chromogen reacts with the PBS present in the cells/tissue (enzymatic detection). Use Tris buffer to wash sections prior to incubating with the substrate. Then wash sections/cells in Tris buffer again after substrate incubation. Pemeabilization has damaged the membrane and removed the membrane protein. Remove permeabilizing agent from your buffers.
Non-specific staining
Primary/secondary antibody concentration may be too high. Try decreasing the antibody concentration and/or the incubation period. Compare signal intensity against cells that do not express the target. Endogenous peroxidases are active. Use enzyme inhibitors i.e. Levamisol (2 mM) for alkaline phosphatase or H2O2 (0.3% v/v) for peroxidase. (See IHC protocol). The primary antibody is raised against the same species as the tissue stained (e.g mouse primary antibody tested on mouse tissue). When the secondary antibody is applied, it binds to all the tissue as it is raised against that species. Use a primary antibody raised against a different species than your tissue. The sections/cells have dried out. Keep sections/cells at high humidity and do not let them dry out.
Further useful Immunohistochemistry/immunocytochemistry protocols

There are many more useful immunohistochemistry/immunocytochemistry procedures and guides on our protocols webpages. Please see the following URL addresses for more information: Double immunofluorescence: sequential protocol www.abcam.com/immunosequential Double immunofluorescence: simultaneous protocol www.abcam.com/immunosimultaneous BrdU immunostaining www.abcam.com/brduimmunostaining Whole mount staining www.abcam.com/wholemountstaining
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SECTION 7: ELISA
7.1 Indirect ELISA
Coat plate with antigen 2 hr RT or 4C overnight
Key
Antigen
Wash plates with PBS 0.2% Tween 20 4 times
Block with 5% serum or BSA 2 hr or overnight 4C
Primary antibody
Incubate with primary antibody 2 hr RT or 4C overnight Wash plates with PBS 0.2% Tween 20 4 times
Conjugated Secondary antibody
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Add conjugated secondary antibody Incubate 1 - 2 hr
Wash plates with PBS 0.2% Tween 20 4 times Substrate
Colored product
Enzymatic detection Follow manufacturers recommendations
Read absorbance on ELISA plate reader and analyze results

Buffers and reagents: For accurate quantitative results, always compare signals of unknown samples against those of a standard curve. Standards (duplicates or triplicates) and blanks must be run with each plate to ensure accuracy. General procedure: Coating antigen to microplate 1. Dilute the antigen to a final concentration of 20 g/ml in PBS or other carbonate buffer. Coat the wells of a PVC microtiter plate with the antigen by pipeting 50 l of the antigen dilution in the top wells of the plate. Dilute down the plate as required.
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Test samples containing pure antigen are usually pipeted onto the plate at less than 2 g/ml. Pure solutions are not essential, but as a guideline, over 3% of the protein in the test sample should be the target protein (antigen). Antigen protein concentration should not be over 20 g/ml as this will saturate most of the available sites on the microtitre plate. Ensure the samples contain the antigen at a concentration that is within the detection range of the antibody.
2. Cover the plate with an adhesive plastic and incubate for 2 hr at room temperature, or 4C overnight. The coating incubation time may require some optimization. 3. Remove the coating solution and wash the plate 3 X by filling the wells with 200 l PBS. Remove the wash solutions by flicking the plate gently over a sink. Remove any remaining drops by patting the plate on a paper towel. Blocking 4. Block the remaining protein binding sites in the coated wells by adding 200 l blocking buffer, 5% non fat dry milk or 5% serum in PBS. Alternative blocking reagents include BlockACE or BSA. 5. Cover the plate with an adhesive plastic and incubate for at least 2 hr at room temperature or if more convenient, overnight at 4C. 6. Wash the plate twice with PBS. Incubation with primary and secondary antibody 7. Add 100 l of diluted primary antibody to each well. 8. Cover the plate with an adhesive plastic and incubate for 2 hr at room temperature. This incubation time may require optimization. Although 2 hr is usually enough to obtain a strong signal, if a weak signal is obtained, stronger staining will often be observed when incubated overnight at 4C. 9. Wash the plate 4 X with PBS. 10. Add 100 l of conjugated secondary antibody, diluted at the optimal concentration (according to the manufacturers instructions) in blocking buffer immediately before use. 11. Cover the plate with an adhesive plastic and incubate for 1-2 hr at room temperature. 12. Wash the plate 4 X with PBS. Detection Although many different types of enzymes have been used for detection, horse radish peroxidase (HRP) and alkaline phosphatase (ALP) are the most widely used enzymes employed in ELISA assay. It is important to consider the fact that some biological materials have high levels of endogenous enzyme activity (such as high ALP in alveolar cells, high peroxidase in red blood cells) and this may result in non specific signal. If necessary, perform an additional blocking treatment with Levamisol (for ALP) or with a 0.3% solution of H2O2 in methanol. ALP substrate For most applications pNPP (p-Nitrophenyl-phosphate) is the most widely used substrate. The yellow color of nitrophenol can be measured at 405 nm after 15-30 min incubation at room temperature (this reaction can be stopped by adding equal volume of 0.75 M NaOH). HRP chromogens The substrate for HRP is hydrogen peroxide. Cleavage of hydrogen peroxide is coupled to oxidation of a hydrogen donor which changes color during reaction. TMB (3,3,5,5-tetramethylbenzidine). Add TMB solution to each well, incubate for 15-30 min, add equal volume of stopping solution (2 M H2SO4) and read the optical density at 450 nm. OPD (o-phenylenediamine dihydrochloride). The end product is measured at 492 nm. Be aware that the substrate is light sensitive so keep and store it in the dark. ABTS (2,2-azino-di-[3-ethyl-benzothiazoline-6 sulfonic acid] diammonium salt). The end product is green and the optical density can be measured at 416 nm.
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Note: some enzyme substrates are considered hazardous (potential carcinogens), therefore always handle with care and wear gloves.
13. Dispense 100 l (or 50 l) of the substrate solution per well with a multichannel pipette or a multipipette. 14. After sufficient color development add 100 l of stop solution to the wells (if necessary). 15. Read the absorbance (optical density) of each well with a plate reader. Analysis of data: Prepare a standard curve from the data produced from the serial dilutions with concentration on the x axis (log scale) vs. absorbance on the y axis (linear). Interpolate the concentration of the sample from this standard curve.
7.2 Direct ELISA protocol General procedure:

Coating antigen to microplate 1. Dilute the antigen to a final concentration of 20 g/ml in PBS or other carbonate buffer. Coat the wells of a PVC microtiter plate with the antigen by pipeting 50 l of the antigen dilution in the top wells of the plate. Dilute down the plate as required.
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Test samples containing pure antigen are usually pipetted onto the plate at less than 2 g/ml. Pure solutions are not essential, but as a guideline, over 3% of the protein in the test sample should be the target protein (antigen). Antigen protein concentration should not be over 20 g/ml as this will saturate most of the available sites on the microtitre plate. Ensure the samples contain the antigen at a concentration that is within the detection range of the antibody.
2. Cover the plate with an adhesive plastic and incubate for 2 hr at room temperature, or 4C overnight. The coating incubation time may require some optimization. 3. Remove the coating solution and wash the plate twice by filling the wells with 200 l PBS. Remove the wash solutions by flicking the plate gently over a sink. Remove any remaining drops by patting the plate on a paper towel. Blocking 4. Block the remaining protein binding sites in the coated wells by adding 200 l blocking buffer, 5% non fat dry milk in PBS per well. Alternative blocking reagents include BlockACE or BSA. 5. Cover the plate with an adhesive plastic and incubate for at least 2 hr at room temperature or if more convenient, overnight at 4C. 6. Wash the plate twice with PBS. Incubation with the antibody 7. Add 100 l of the antibody, diluted at the optimal concentration (according to the manufacturers instructions) in blocking buffer immediately before use. 8. Cover the plate with an adhesive plastic and incubate for 2 hr at room temperature. This incubation time may require optimization. Although 2 hr is usually enough to obtain a strong signal, if a weak signal is obtained, stronger staining will often be observed when incubated overnight at 4C. 9. Wash the plate 4 X with PBS. Detection 10. Dispense 100 l (or 50 l) of the substrate solution per well with a multichannel pipette or a multipipette. 11. After sufficient color development add 100 l of stop solution to the wells (if it is necessary). Read the absorbance (optical density) of each well with a plate reader.
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Analysis of data: Prepare a standard curve from the data produced from the serial dilutions with concentration on the x axis (log scale) vs. absorbance on the y axis (linear). Interpolate the concentration of the sample from this standard curve.
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7.3 Sandwich ELISA

Incubate with coating antibody in bicarbonate buffer Overnight 4C Wash plates with PBS 0.2% Tween 20 2 X Primary capture antibody Primary detection antibody Add sample to wells Dilute down the plate Conjugated Secondary antibody Wash plates with PBS 0.2% Tween 20 2 X
Key
Antigen
Block with 5% serum or BSA for 2 hr or overnight 4C
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Incubate with detection antibody 2 hr RT
Wash with PBS 0.2% Tween 20 4 X
Incubate with conjugated secondary antibody 30 min to 2 hr RT
Wash plates with PBS 0.2% Tween 20 4 X Colored product
Substrate
Enzymatic detection Follow manufacturers recommendations
Read absorbance on ELISA plate reader and analyze results
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The sandwich ELISA measures the amount of antigen between two layers of antibodies (i.e. capture and detection antibody). The antigen to be measured must contain at least two antigenic sites capable of binding to antibody, since at least two antibodies act in the sandwich. Either monoclonal or polyclonal antibodies can be used as the capture and detection antibodies in sandwich ELISA systems. Monoclonal antibodies recognize a single epitope that allows fine detection and quantification of small differences in antigen. A polyclonal is often used as the capture antibody to pull down as much of the antigen as possible. The advantage of sandwich ELISA is that the sample does not have to be purified before analysis, and the assay can be very sensitive (up to two to five times more sensitive than direct or indirect). General note: Sandwich ELISA procedures can be difficult to optimise and tested match pair antibodies should be used. This ensures the antibodies are detecting different epitopes on the target protein so they do not interfere with the other antibody binding. Therefore, we are unable to guarantee our antibodies in sandwich ELISA unless they have been specifically tested for sandwich ELISA. Please review antibody datasheets for information on tested applications. General procedure: Coating with capture antibody 1. Coat the wells of a PVC microtiter plate with the capture antibody at a concentration of 1-10 g/ml in carbonate/bicarbonate buffer (pH 7.4).
If an unpurified antibody is used (e.g. ascites fluid or antiserum), you may need to compensate for the lower amount of specific antibody by increasing the concentration of the sample protein (try 10 g/ml).
2. Cover the plate with an adhesive plastic and incubate overnight at 4C.
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3. Remove the coating solution and wash the plate twice by filling the wells with 200 l PBS. Remove the wash solutions by flicking the plate gently over a sink. Remove any remaining drops by patting the plate on a paper towel. Blocking and adding samples 4. Block the remaining protein binding sites in the coated wells by adding 200 l blocking buffer, 5% non fat dry milk in PBS, per well. 5. Cover the plate with an adhesive plastic and incubate for at least 1-2 hr at room temperature or if more convenient, overnight at 4C. 6. Add 100 l of appropriately diluted samples to each well. For accurate quantitative results, always compare signal of unknown samples against those of a standard curve. Standards (duplicates or triplicates) and blank must be run with each plate to ensure accuracy. Incubate for 90 min at 37C.
For quantification, the concentration of the standard used should span the most dynamic detection range of antibody binding. You may need to optimize the concentration range to ensure you obtain a suitable standard curve. For accurate quantfication, always run samples and standards in duplicate or triplicate.
7. Remove the samples and wash the plate twice by filling the wells with 200 l PBS. Incubation with detection antibody and then secondary antibody 8. Add 100 l of diluted detection antibody to each well.
Ensure the secondary detection antibody recognizes a different epitope on the target protein than the coating antibody. This prevents interference with the antibody binding and ensures the epitope for the second antibody is available for binding. Use a tested matched pair whenever possible.
9. Cover the plate with an adhesive plastic and incubate for 2 hr at room temperature. 10. Wash the plate 4 X with PBS. 11. Add 100 l of conjugated secondary antibody, diluted at the optimal concentration (according to the manufacturers instructions) in blocking buffer immediately before use.
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12. Cover the plate with an adhesive plastic and incubate for 1-2 hr at room temperature. 13. Wash the plate 4 X with PBS. Detection Although many different types of enzymes have been used for detection, horse radish peroxidase (HRP) and alkaline phosphatase (AP) are the two most widely used enzymes employed in ELISA assay. It is important to consider the fact that some biological materials have high levels of endogenous enzyme activity (such as high AP in alveolar cells, high peroxidase in red blood cells) and this may result in a non-specific signal. If necessary, perform an additional blocking treatment with Levamisol (for AP) or with 0.3% solution of H2O2 in methanol (for peroxidase). ALP substrate For most applications pNPP (p-Nitrophenyl-phosphate) is the most widely used substrate. The yellow color of nitrophenol can be measured at 405 nm after 15-30 min incubation at room temperature (this reaction can be stopped by adding equal volume of 0.75 M NaOH). HRP chromogenes The substrate for HRP is hydrogen peroxide. Cleavage of hydrogen peroxide is coupled to oxidation of a hydrogen donor which changes color during reaction. TMB (3,3,5,5-tetramethylbenzidine). Add TMB solution to each well, incubate for 15-30 min, add an equal volume of stopping solution (2 M H2SO4) and read the optical density at 450 nm. OPD (o-phenylenediamine dihydrochloride). The end product is measured at 492 nm. Be aware that the substrate is light sensitive so keep and store it in the dark. ABTS (2,2-azino-di-[3-ethyl-benzothiazoline-6 sulfonic acid] diammonium salt). The end product is green and the optical density can be measured at 416 nm.
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14. Dispense 100 l (or 50 l) of the substrate solution per well with a multichannel pipette or a multipipette. Analysis of data: Prepare a standard curve from the data produced from the serial dilutions with concentration on the x axis (log scale) vs. absorbance on the y axis (linear). Interpolate the concentration of the sample from this standard curve.
7.4 Troubleshooting tips - ELISA Positive results in negative control

Contamination of reagents/samples May be contamination of reagents or samples, or cross contamination from splashing between wells. Use fresh reagents and pipette carefully. Sandwich ELISA detection antibody is detecting coating antibody Check the correct coating antibody and detection antibodies are being used and that they will not detect each other. Insufficient washing of plates Ensure wells are washed adequately by filling them with wash buffer. Ensure all residual antibody solutions are removed before washing. Too much antibody used leading to non specific binding Check the recommended amount of antibody suggested. Try using less antibody.
High background across entire plate

Conjugate too strong or left on too long Check dilution of conjugate, use it at the recommended dilution. Stop the reaction using stop buffer as soon as the plate has developed enough for absorbance readings. Substrate solution or stop solution is not fresh Use fresh substrate solution. Stop solution should be clear (if it has gone yellow, this is a sign of contamination and it should be replaced).
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Reaction not stopped Color will keep developing if the substrate reaction is not stopped. Plate left too long before reading on the plate reader Color will keep developing (though at a slower rate if stop solution has been added). Contaminants from laboratory glassware Ensure reagents are fresh and prepared in clean glassware. Substrate incubation carried out in the light Substrate incubation should be carried out in the dark. Incubation temperature too high Antibodies will have optimum binding activity at the correct temperature. Ensure the incubations are carried out at the correct temperature and that incubators are set at the correct temperature and working. Incubation temperature may require some optimization. Non specific binding of antibody Ensure a block step is included and a suitable blocking buffer is being used. We recommend using 5 to 10% serum from the same species as the secondary antibody, or bovine serum. Ensure wells are pre-processed to prevent non specific attachment. Use an affinity purified antibody, preferably pre-absorbed. Also check suggestions listed under Positive results in negative control
Low absorbance values

Target protein not expressed in sample used or low level of target protein expression in sample used Check the expression profile of the target protein to ensure it will be expressed in your samples. If there is low level of target protein expression, increase the amount of sample used or you may need to change to a more sensitive assay. Ensure you are using a positive control within the detection range of the assay. Insufficient antibody Check the recommended amount of antibody is being used. The concentration of antibody may require increasing for optimization of results. Substrate solutions not fresh or combined incorrectly Prepare the substrate solutions immediately before use. Ensure the stock solutions are in date and have been stored correctly, and are being used at the correct concentration. Ensure the reagents are used as directed at the correct concentration. Reagents not fresh or not at the correct pH Ensure reagents have been prepared correctly and are in date. Incubation time not long enough Ensure you are incubating the antibody for the recommended amount of time if an incubation time is suggested. The incubation time may require increasing for optimization of results. Incubation temperature too low Antibodies will have optimum binding activity at the correct temperature. Ensure the incubations are carried out at the correct temperature and that incubators are set at the correct temperature and are working. Incubation temperature may require some optimization. Ensure all reagents are at room temperature before proceeding. Stop solution not added Addition of stop solution increases the intensity of color reaction and stabilizes the final color reaction.
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High absorbance values

High absorbance values for samples and/or positive control. Absorbance is not reduced as the sample is diluted down the plate The concentration of samples or positive control is too high and out of range for the sensitivity of the assay. Re-assess the assay you are using OR reduce the concentration of samples and control by dilution before adding to the plate. Consider the dilution when calculating the resulting concentrations.
Inconsistent absorbances across the plate

Plates stacked during incubations Stacking of plates does not allow even distribution of temperature across the wells of the plates. Avoid stacking.
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Pipetting inconsistent Ensure pipettes are working correctly and are calibrated. Ensure pipette tips are pushed on far enough to create a good seal. Take particular care when diluting down the plate and watch to make sure the pipette tips are all picking up and releasing the correct amount of liquid. This will greatly affect consistency of results between duplicates. Antibody dilutions / reagents not well mixed To ensure a consistent concentration across all wells, ensure all reagents and samples are mixed before pipetting onto the plate. Wells allowed to dry out Ensure lids are left on the plates at all times when incubating. Place a humidifying water tray (bottled clean, sterile water) in the bottom of the incubator. Inadequate washing This will lead to some wells not being washed as well as others, leaving different amounts of unbound antibody behind which will give inconsistent results. Bottom of the plate is dirty affecting absorbance readings. Clean the bottom of the plate carefully before re-reading the plate.
Color developing slowly

Plates are not at the correct temperature Ensure plates are at room temperature and that the reagents are at room temperature before use. Conjugate too weak Prepare the substrate solutions immediately before use. Ensure the stock solutions are in date and have been stored correctly, and are being used at the correct concentration. Ensure the reagents are used as directed, at the correct concentration.
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Contamination of solutions Presence of contaminants, such as sodium azide and peroxidases can affect the substrate reaction. Avoid using reagents containing these preservatives.
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SECTION 8: Flow Cytometry

Flow cytometry is now a widely used method for analyzing expression of cell surface and intracellular molecules, characterizing and defining different cell types in heterogeneous cell populations, assessing the purity of isolated subpopulations, and analyzing cell size and volume. It allows simultaneous multi parameter analysis of single cells. It is predominantly used to measure fluorescence intensity produced by fluorescent labeled antibodies detecting proteins or ligands that bind to specific cell associated molecules, such as DNA binding by Propidium Iodide (PI). The staining procedure involves making a single cell suspension from cell culture or tissue samples. The cells are then incubated in tubes or microtiter plates with unlabeled or fluorescent labeled antibodies. Cells are then analyzed on the flow cytometer.
The Flow Cytometer:

Sample (stained cells in suspension)
Sheath fluid
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Nozzle
Hydrodynamic Focusing Cells pass through in 'single file'
Fluorescence emitted from stained cells detected
Forward and side scattered light from all cells detected Laser light source
When the stained cell sample in suspension buffer is run through the cytometer, it is hydrodynamically focused using sheath fluid, through a very small nozzle. The tiny stream of fluid takes the cells past the laser light one cell at a time. There are a number of detectors to detect the light scattered from the cells/particles as they go though the beam. There is one in front of the light beam (Forward Scatter or FSC) and several side on to it (Side Scatter or SSC). Fluorescent detectors are used for the detection of fluorochromes themselves.
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Particles/cells passing through the beam will scatter the light, which is detected as forward scatter and side scatter. The combination of scattered and fluorescent light is detected and analyzed. Forward Scatter correlates with the cell size and Side Scatter depends on the density of the particle/cell (i.e. number of cytoplasmic granules, membrane size), and in this manner cell populations can often be distinguished based on their difference in size and density. Fluorochromes used for detection or staining will emit light when excited by a laser with the corresponding excitation wavelength. These particles/cells can be detected individually and the data analyzed.
Direct staining:
In direct imunofluorescence staining, cells are incubated with an antibody directly conjugated to a fluorochrome (e.g. FITC). This has the advantage of requiring only one antibody incubation step and eliminates the possibility of non specific binding from a secondary antibody. It is particularly useful for intracellular staining, where large antibody-fluorochrome complexes including secondary antibodies can become trapped causing non specific binding, or even fail to enter the cell and prevent primary antibody detection.
Indirect staining:
In indirect staining, the primary antibody is not fluorochrome labeled but is detected by a second fluorochrome labeled antibody. Alternatively, the avidin-biotin system can be used, whereby an antibody is conjugated to biotin and detected with fluorochrome labeled avidin. With the wide range of conjugated secondary antibodies now available, this method means that unconjugated primary antibodies raised against many different targets can be used in conjunction with a labeled secondary antibody for flow cytometry analysis. This widens the choice of target proteins for the researcher.
Intracellular staining:
Staining of intracellular antigens for flow cytometry depends on various fixation and permeabilization methods to allow access of antibodies to internal cellular proteins. A successful staining procedure in all cases is dependent on optimization of experimental conditions through titering of antibodies, use of appropriate controls to set up the flow cytometer correctly, and optimized fixation and permeabilization methods if necessary.
Selecting a fluorochrome conjugate SECTION 8

The ability of a given antibody to resolve a positive from a negative often depends on which fluorochrome conjugate is used. A general guideline for the relative intensities of the various fluorochromes is, from brightest to dimmest, PE (phycoerythrin), PE-Cy7, PECy5, APC > APC-Cy7, Alexa Fluor 47, Alexa Fluor 700 > FITC, Pacific Blue, Alexa Fluor 488. This is a general pattern when using signal noise ratio. Some differences are seen for individual antibodies. A highly expressed antigen will usually be resolved with almost any fluorophore. An antigen expressed at lower density might require the higher signal;background ratio provided by a brighter PE or APC conjugate to separate the positive cells adequately from the unstained cells. The relative fluorochrome intensity depends on the instrument. This is because of differences in the laser and filter combinations used on the different instruments. Be sure to use the appropriate FACS instrument.
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8.1 Recommended controls for Flow Cytometry / FACS

Along with the samples to be labeled, the following controls should be used whenever possible. The various positive controls are used for compensating and gating when setting up the flow cytometer.
Control Cells only. Use treated and untreated cells
Sample type
Primary Ab
Secondary
Reason
Negative control cells
No
No
Negative Control/Background Autofluoresence control
Primary Ab control
Yes
No
Check for non specific binding of primary
Treated primary Ab control
Treated cells
No
Yes
Check for non specific binding of secondary Ab on treated cells
Isotype control
Use Isotype control antibody. This should be the same antibody isotype as primary antibody.
Yes
To confirm that the primary antibody binding is specific and not a results of non-specific Fc receptor binding or other protein interactions.
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Compensation controls for each fluorochrome
Positive population of labelled beads or positive control cell sample
Yes
Yes
Positive control to set up cytometer alignment and to remove spectral overlap. Nonviable cells can be discriminated from live cells on the basis of light scatter (FSC=forward scatter). This discrimination is often lost in fixed or permeabilized cells. In these cases dead cells can be distinguished from live cells by their uptake of fluorescent DNA dyes due to loss of membrane integrity e.g. PI (propidium iodide) is used for dead-cell discrimination in unfixed and non permeabilized cells. 7-AAD (7-aminoactinomycin D, fluorescent) + AD (actinomycin D, nonfluorescent) for fixed or permeabilized cells.
Cell viability control
Cell sample (identical to other samples) stained with both antibody and PI nuclear stain
Yes
Yes
Specificity control
Cell samples
Add excess unlabelled primary antibody with normal Yes. With excess nonFor direct amount of labelled primary. If staining is specific, the labelled primary. staining only non-labelled primary should compete with labelled primary and reduce the fluorescence observed. Check for non specific binding of secondary Ab on treated cells
Treated secondary Ab control
Treated cells
No
Yes
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8.2 Direct staining protocol (cell surface staining)
1x105 to 1x106 cells per 100 l sample ice cold
Key
Cell
Antigen
Fluorochrome conjugated Primary antibody
Wash with PBS 0.2% Tween 20, 4 X centrifuge 400 g for 5 min Block with 5% serum or BSA for 15 to 30 min Wash with PBS 0.2% Tween 20, 4 X centrifuge 400 g for 5 min
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Incubate with fluorochrome conjugated primary antibody 15 to 45 min 4C in the dark 0.1-10 g antibody / ml
Fix: (optional) Add 100 l fixative (eg 4% PFA) to each tube 15 min 4C Wash in PBS 0.2% Tween 20, 4 X centrifuge 400 g for 5 min Resuspend to 500 l to 1 ml in ice cold PBS, 10% FCS, 1% sodium azide Store at 4C until analysis (within 24 hr) Run and analysis on Flow Cytometer
General procedure:
1. Harvest, wash the cells and adjust cell suspension to a concentration of 1-5 x 106 cells/ml in ice cold PBS, 10% FCS, 1% sodium azide. Cells are usually stained in polystyrene round bottom 12 x 75 mm2 Falcon tubes. However, they can be stained in any container for which you have an appropriate centrifuge e.g. test tubes, eppendorf tubes, and 96 well round bottomed microtiter plates. In general, cells should be centrifuged sufficiently so the supernatant fluid can be removed with little loss of cells, but not so the cells are difficult to resuspend.
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We recommend to stain with ice cold reagents and solutions and at 4C as a low temperature and presence of sodium azide prevent the modulation and internalization of surface antigens which can produce a loss of fluorescence intensity.
2. Add 0.1-10 g/ml of the primary labeled antibody. Dilutions, if necessary, should be made in 3% BSA/PBS (propidium iodide can also be added at this point for dead cell exclusion). 3. Incubate for at least 30 min at room temperature or 4C. This step will require optimization. 4. Wash the cells 3 X by centrifugation at 400 g for 5 min and resuspend them in 500 l to 1 ml of ice cold PBS, 10% FCS,1% sodium azide. Keep the cells in the dark on ice or at 4C in a fridge until your scheduled time for analysis. 5. For best results, analyze the cells on the flow cytometer as soon as possible.
We recommend analysis on the same day. For extended storage (16 hr) as well as for greater flexibility in planning time on the cytometer, resuspend cells in 1% paraformaldehyde to prevent deterioration
Fixation:
If you need to wait longer than 1 hour, you may need to fix the cells after step 3. This can preserve them for several days (this will stabilize the light scatter and inactivate most biohazardous agents). Controls will require fixation using the same procedure. Cells should not be fixed if they need to remain viable. There are several methods available, please refer to fixation in the indirect staining protocol. The fixation for different antigens will require optimization by the user.
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8.3 Indirect staining protocol (cell surface staining)

Indirect labeling requires two incubation steps, firstly with a primary antibody then with a compatible secondary antibody. The secondary (and not the primary) antibody has the fluorescent dye (FITC, PE, Cy5, etc.) conjugated. Please note that this is a general protocol and you may need to adapt it for your applications.
General procedure:
1. Harvest and wash the cells then determine the total cell number. Cells are usually stained in polystyrene round bottom 12 x 75 mm2 Falcon tubes. However, they can be stained in any container for which you have an appropriate centrifuge e.g. test tubes, eppendorf tubes, and 96 well round bottomed microtiter plates. In general, cells should be spun down hard enough that the supernatant fluid can be removed with little loss of cells, but not so hard that the cells are difficult to resuspend. It is always useful to check the viability of the cells which should be around 95% not less than 90%. 2. Resuspend the cells to approximately 1-5 x 106 cells/ml in ice cold PBS, 10% FCS, 1% sodium azide.
Use ice cold reagents and solutions and at 4C a low temperature and presence of sodium azide prevent the modulation and internalization of surface antigens which can produce a loss of fluorescence intensity.
3. Add 100 l of cell suspension to each tube. 4. Add 0.1-10 g/ml of the primary antibody. Dilutions, if necessary, should be made in 3% BSA / PBS. 5. Incubate for at least 30 min at room temperature or 4C in the dark. 6. Wash the cells by centrifugation at 400 g for 5 min and resuspend them in ice cold PBS. You may need to adjust the conditions of the centrifugation (the force and the time) for the cell types used. 7. Dilute the fluorochrome labeled secondary antibody in 3% BSA/PBS at the optimal dilution (according to the manufacturers instructions) and then resuspend the cells in this solution. 8. Incubate for at least 20-30 min at room temperature of 4C. This incubation must be done in the dark.
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9. Wash the cells 3 X by centrifugation at 400 g for 5 min and resuspend them in ice cold PBS, 3% BSA, 1% sodium azide. 11. Store the cell suspension immediately at 4C in the dark. 12. For best results, analyze the cells on the flow cytometer as soon as possible.
We recommend analysis on the same day. For extended storage (16 hr) as well as for greater flexibility in planning time on the cytometer, resuspend cells in 1% paraformaldehyde to prevent deterioration.
Fixation:
If you need to wait longer than 1 hour before analysis, you may need to fix the cells after step 5. This can preserve them for several days (this will stabilize the light scatter and inactivate most biohazardous agents). Controls will required fixation using the same procedure. Cells should not be fixed if they need to remain viable. There are several methods available. The fixation for different antigens will require optimization by the user. 1. Paraformaldehyde 0.01% to 1% for 10-15 min only, 100 l per sample. 2. Acetone or methanol:
Note: polystyrene/plastic tubes are not suitable for use with acetone
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Add 1 ml ice cold acetone to each sample. Mix gently. Place at -20C for 5-10 min. Centrifuge, wash twice in PBS 1% BSA
Do not add sodium azide to buffers if you are concerned with recovering cell function e.g. if cells are to be collected for functional assays as it inhibits metabolic activity.
8.4 Intracellular staining

1x105 to 1x106 cells per 100 l sample ice cold
Key
Cell
Antigen
Fluorochrome conjugated Primary antibody
Fix: Add 100l fixative (eg 4% PFA) to each tube 15 min 4C Wash with PBS 0.2% Tween 20, 4 centrifuge 400 g for 5 min (Continued Overleaf)
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Permeabilize Add 100 l permeabilizing agent to each tube. Incubate 15min 4C 0.2% Saponin or 0.2% Digitonin
Wash with PBS 0.2% Tween 20, 4 X centrifuge 400 g for 5 min Block with 5% serum or BSA for 15 to 30 min Wash with PBS 0.2% Tween 20, 4 X centrifuge 400 g for 5 min
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Incubate with fluorochrome conjugated primary antibody 15 to 45 min 4C in the dark 0.1-10 g antibody / ml
Wash with PBS 0.2% Tween 20, 4 X centrifuge 400 g for 5 min Resuspend to 500 l to 1ml in ice cold PBS, 10% FCS, 1% sodium azide Store at 4C until analysis (within 24hr) Analysis on Flow Cytometer
Fixing and permeabilization:

For intracellular staining, cells can be fixed first to ensure stability of soluble antigens or antigens with a short half life (see below for important exceptions). This should retain the target protein in the original cellular location. Detection of intracellular antigens requires a cell permeabilization step prior to staining. Antibodies should be prepared in permeabilization buffer to ensure the cells remain permeable. When gating on cell populations, the light scatter profiles of the cells on the flow cytometer will change considerably after permeabilization.
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Note: Cell surface staining should be performed prior to fixation.
There are several methods available: 1. Formaldehyde followed by detergent Fixation in 0.01% formaldehyde for 10-15 min (this will stabilize proteins), followed by disruption of membrane by detergent. Detergents: Triton or NP-40 (0.1 to 1% in PBS). These will also partially dissolve the nuclear membrane and are therefore very suitable for nuclear antigen staining. It should be noted that loss of cell membrane and cytoplasm will result in decreased light scattering and also in reduced non specific fluorescence. Tween 20, Saponin, Digitonin and Leucoperm are mild membrane solubilisers. Use at 0.5% v/v in PBS. These give large enough pores for antibodies to go through without dissolving plasma membrane. Suitable for antigens in the cytoplasm or the cytoplasmic face of the plasma membrane. Also suitable for soluble nuclear antigens. 2. Formaldehyde (0.01%) followed by methanol (See step 3). 3. Methanol followed by detergent. Add 1 ml ice cold methanol to each sample. Mix gently. Place at -20C for 10 min. Centrifuge, wash twice in PBS 1% BSA. 4. Acetone fixation and permeabilization: Add 1 ml ice cold acetone to each sample. Mix gently. Place at -20C for 5 to 10 min. Centrifuge, wash twice in PBS 1% BSA.
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Note: Polystyrene or plastic tubes are not suitable for use with acetone.
Special recommendations: Antigens close to the plasma membrane and soluble cytoplasmic antigens will require mild cell permeabilization without fixation. Cytoskeletal, viral and some enzyme antigens usually give optimal results when fixed with acetone, alcohol or formaldehyde (high concentration). Antigens in cytomplasmic organelles and granules will require a fixation and permeabilization method depending on the antigen. The epitope needs to remain accessible.
Intracellular staining procedure:

1. Add 100 l of fixative. Incubate for 10 min at required temperature (see above). 2. Add 100 l detergent based permeabilizing agent and incubate in the dark at room temperature for 15 min. 3. Wash the cells by adding 2 ml of PBS (containing 0.1% triton or other permeabilizing detergent), centrifuge at 300 g (2000 rpm) for 5 min, discard supernatant and re-suspend the pellet in the volume remaining. 4. Follow the antibody staining procedure as indicated in our direct and indirect protocols.
Antibodies should be prepared in permeabilization buffer to ensure the cells remain permeable.
Detection of secreted proteins:

Detection of secreted proteins is difficult as the protein will be released from the cell before detection, or may degrade rapidly. Brefaldin A and other compounds are often used as a Golgi-block. Cells are incubated with Brefaldin A which prevents proteins being released from the golgi. Any cells expressing the protein can then be detected.
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8.5 Troubleshooting tips - Flow cytometry No signal / weak fluorescence intensity

Signal not correctly compensated Check positive single color control is set up correctly on flow cytometer, gated and compensated correctly to capture all the events. Insufficient antibody present for detection Increase amount/concentration of antibody. Intracellular target not accessible Check if target protein is intracellular. For internal staining, ensure adequate permeabilization. To prevent internalization of cell surface proteins, the procedure should be carried out on ice or at 4C, with ice cold reagents, to stop all reactions. Adding sodium azide will prevent the modulation and internalization of surface antigens which can produce a loss of fluorescence intensity. For staining of cell lines, trypsin can often induce internalization of cell surface proteins, particularly cell surface molecules, and more gentle detachment methods may be required. Intracellular staining-fluorochrome conjugate too large Fluorochromes for intracellular staining experiments should have low molecular weight. Large molecular weight fluorochromes can reduce antibody motility and possibly its entry into the cell. Lasers not aligned Ensure lasers on the flow cytometer are aligned correctly by running flow check beads and adjusting alignment if necessary. If the lasers do not align correctly or if drift occurs, you may need to consider having the machine serviced. Target protein not present or expressed at low level Ensure tissue or cell type expresses target protein and that it is present in a high enough amount to detect. Soluble or secreted target protein Is the target protein soluble and secreted from the cell? It needs to be membrane bound or cytoplasmic to be detected easily by flow cytometry. A Golgi-block step, such as with Brefaldin A, may improve the signal achieved for intracellular staining. Offset too high or gain too low Use the positive control to set up the flow cytometer correctly again, using the offset to ensure the fluorescent signal from cells is not being cut off, and increase the gain to increase the signal (within reason care should be taken ). Fluorochrome fluorescence has faded Antibody may have been kept for too long or left out in the light. Fresh antibody will be required. The primary antibody and the secondary antibody are not compatible Use a secondary antibody that was raised against the species in which the primary was raised (e.g. primary is raised in rabbit, use antirabbit secondary).
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High fluorescence intensity

Antibody concentration too high This will give high non-specific binding or very high intensity of fluorescence. Reduce the amount of antibody added to each sample. Excess antibody trapped This can be a particular problem in intracellular staining where large fluorochrome molecules on the antibody can be trapped. Ensure adequate washing steps and include Tween or Triton in wash buffers. Inadequate blocking Add 1% to 3% blocking agent with antibody as well as a blocking step.
High background or high percentage of positive cells

Gain set too high or offset too low Use the positive control to set up the flow cytometer correctly again, using the offset to reduce background from small particles and reduce the gain to decrease the signal. Excess antibody Decrease the antibody concentration. You can also add detergent to the wash buffers to ensure washing away of excess antibody.
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Two or more cell populations observed when there should be just one
More than one cell population present expressing target protein Check expected expression levels from the cell types contained in the sample and ensure adequate cell separation if necessary. Cell doublets present Doublets of cells will show as a second cell population at approximately twice the fluorescence intensity on the plot. Mix cells gently before staining and again before running on the flow cytometer using a pipette. Cells can also be sieved or filtered to remove clumps (30 m Nylon Mesh).
High side scatter background (from small particles)

Cells lysed Ensure cells in the sample have not lysed and broken up. Samples should be fresh and prepared correctly. Do not centrifuge cells at a high rotor speed or vortex too violently. Bacterial contamination Ensure sample is not contaminated. Bacteria will auto fluoresce at low level. This will also give a high event rate.
Low event rate

Low number of cells/ml Run 1 x 106 cells/ml. Ensure cells are mixed well (but gently). Cells clumped, blocking tubing Ensure a homologous single cell suspension by pipetting gently several times before staining. Ensure you mix again before running. In extreme cases, cells can be sieved or filtered to remove clumps (30 m Nylon Mesh).
High event rate SECTION 8

High number of cells Dilute to between 1 x 105 and 1 x 106 cells/ml
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SECTION 9: Immunoprecipitation (IP) protocol

Immunoprecipitation procedure
Immunoprecipitation is a method that enables the purification of a protein. An antibody for the protein of interest is incubated with a cell extract enabling the antibody to bind to the protein in solution. The antibody/antigen complex will then be pulled out of the sample using protein A/G-coupled agarose beads. This physically isolates the protein of interest from the rest of the sample. The sample can then be separated by SDS-PAGE for western blot analysis.
9.1.1.a Lysis buffers

The ideal lysis buffer will leave proteins in their native conformation, minimizing denaturation of antibody binding sites while at the same time releasing adequate amounts of protein from the sample for subsequent analysis. Non ionic detergents such as NP-40 and Triton X100 are less harsh than ionic detergents such as SDS and sodium deoxycholate. Other variables that can affect the success of IP include salt concentration, divalent cation concentration, and pH. Therefore to optimize these variables they should be tested within the following ranges (From Harlow and Lane, page 231; see References page 67): 0-1 M Salts 0.1-2% detergent, non-ionic 0.01-0.5% Detergent, ionic 0-10 mM Divalent cations 0-5 mM EDTA pH: 6-9 The recipe for various lysis buffers can be found in the buffers section 11, page 77. Denaturing lysis buffer Use for antigens that are detergent soluble and can be recognized in native form by the antibody. 1. RIPA (Radio Immuno Precipitation Assay) buffer More denaturing than NP-40 or Triton X-100 lysis buffer, RIPA buffer contains the ionic detergents SDS and sodium deoxycholate as active constituents and is particularly useful for nuclear membrane disruption for nuclear extracts. RIPA buffer gives low background but can denature some proteins, including kinases. 2. Detergent free soluble protein lysis buffer Use PBS containing EDTA and sodium azide. Some soluble proteins may not require use of detergents. Use this buffer with mechanical breakage of cells, e.g. repeated passage through a syringe or homogenization with a Dounce homogenizer. Denaturing lysis buffer or buffer for non detergent soluble antigens: Epitopes of native proteins are not always accessible to antibodies that only recognize denatured proteins. When harvesting and lysing the cells, heat the cells in denaturing lysis buffer. This method can also be used for antigens that cannot be extracted from the cell with non ionic detergents. Use of DNase1 will aid extraction of proteins from chromatin.
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9.1.1.b Other reagents

Protease inhibitors As soon as lysis occurs, proteolysis, dephosphorylation and denaturation begin. These events can be slowed down tremendously if samples are kept on ice or at 4C at all times and appropriate inhibitors are added fresh to the lysis buffer. Mixtures (cocktails) of protease and phosphatase inhibitors are commercially available. If not using a cocktail, two of the most commonly used protease inhibitors for IP are PMSF (50 ug/ml) and aprotinin (1 g/ml). For more details of protease and phosphatase inhibitors, please see our western blot guide. Other reagents required: Sterile PBS pH 7.4 Sterile PBS-BSA 1% w/v (filtered) TBST buffer Loading/sample buffer for western blotting 100 mM EDTA stock solution is made with 1.86 g EDTA dissolved into 40 ml H2O. Add NaOH to adjust the pH to 7.4. Finally, adjust the total volume to 50 ml.
9.1.2. Preparation of lysates

Lysates from cell culture Non denaturing: 1. Place the cell culture dish on ice and wash the cells with ice cold PBS. 2. Drain the PBS, then add ice cold lysis buffer (1ml per 107 cells/100 mm2 dish/150 cm2 flask; 0.5 ml per 5x106 cells/60 mm2 dish or 75cm2 flask). 3. Scrape adherent cells off the dish using a cold plastic cell scraper then gently transfer the cell suspension into a pre-cooled micro centrifuge tube.
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4. Maintain constant agitation for 30 min at 4C. 5. Centrifuge in a micro centrifuge at 4C. You may have to vary the centrifugation force and time depending on the cell type. A guideline is 20 min at 12,000 rpm but this must be determined by the end user (e.g. leukocytes need a very light centrifugation). 6. Gently remove the tubes from the centrifuge and place on ice. Aspirate the supernatant and place in a fresh tube kept on ice, and discard the pellet. Denaturing: 1. Add 100 l denaturing lysis buffer to 0.5 to 2 x 107 cells. 2. Mix well by vortexing vigorously for 2 to 3 sec at maximum speed. Transfer the cell suspension to a micro centrifuge tube.
The solution can be viscous at this stage due to release of DNA.
3. Heat samples to 95C for 5 min to denature. 4. Dilute the suspension with 0.9 ml non denaturing lysis buffer. Mix gently. (The excess 1% Triton X-100 in the non denaturing lysis buffer quenches the SDS in the original denaturing buffer). 5. Fragment the DNA by passing the lysed suspension 5 to 10 times through a needle attached to a 1 ml syringe.
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Repeat mechanical disruption until the viscosity is reduced to manageable levels. If the DNA is not fully digested and fragmented, it can interfere with the separation of the pellet and supernatant following centrifugation.
6. Incubate on ice for 5 min. 7. Proceed with the immunoprecipitation Lysates from tissue 1. Dissect the tissue of interest with clean tools, on ice preferably, and as quickly as possible to prevent degradation by proteases. 2. Place the tissue in round bottom micro centrifuge tubes and immerse in liquid nitrogen to snap freeze. Store samples at -80C for later use or keep on ice for immediate homogenization. 3. For a ~5 mg piece of tissue, add ~300 l lysis buffer rapidly to the tube and homogenize with an electric homogenizer. 4. Rinse the blade twice with another 300 l lysis buffer per rinse and then maintain constant agitation for 2 hr at 4C (e.g. place on an orbital shaker in the refrigerator). Volumes of lysis buffer must be determined in relation to the amount of tissue present. Protein extract should not be too dilute in order to avoid loss of protein and to minimize the volume of samples to be loaded onto gels. The minimum concentration is 0.1 mg/ml; optimal concentration is 1-5 mg/ml.
Note: If denatured samples are required, use denaturing lysis buffer and perform steps 2 to 5 from the denaturing protocol above.
3. Centrifuge for 20 min at 12,000 rpm at 4C in a micro centrifuge. Gently remove the tubes from the centrifuge and place on ice, aspirate the supernatant and place in a fresh tube kept on ice. Discard the pellet.
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9.1.3. Pre-clearing the lysates

Pre-clearing the lysate can help reduce non specific binding of proteins to agarose or Sepharose beads. Pre-clearing with an irrelevant antibody or serum will remove proteins that bind immunoglobulins non specifically. The end result will have a lower level of background and an improved signal to noise ratio. However, if the final detection of the protein is by western blotting, pre-clearing may not be necessary, unless a contaminating protein is interfering with visualization of the protein of interest. 1. Add either 50 l of irrelevant antibody of the same species and isotype as the IP antibody or normal serum (rabbit is preferred by some researchers, see Harlow and Lane, page 243) to 1 ml of lysate. Incubate for 1 hr on ice. 2 Add 100 l of bead slurry to the lysate. 3. Incubate for 10 to 30 min at 4C with gentle agitation. 4. Spin in micro centrifuge at 14,000 x g at 4C for 10 min. 4. Discard bead pellet and keep supernatant for immunoprecipitation. To increase the yield, the beads can be washed 1 or 2 more times in lysis buffer, and the supernatants collected together. It is important to make sure that as much of the normal serum is removed as possible as this will compete with the specific antibody against the antigen of interest. To check for this, a test can be done with lysis buffer instead of sample, performing all pre-clearing steps as above. A coomassie stain of a gel in which the resulting supernatant is run will reveal if the serum Ig is being removed effectively. If serum has not been sufficiently removed, bands will be present at 50 and 25 kDa for heavy and light chains, its presence may contribute to a weak IP. Consider either decreasing the amount of serum or increasing the amount of beads incubated with your samples in the preclearing step.
9.1.4. Immunoprecipitation
1. On ice, in a micro centrifuge tube add 10-50 g cell lysate plus the recommended amount of antibody. These amounts will be chosen depending on the abundance of the protein and the affinity of the antibody for the protein. Typically in a pilot experiment a fixed amount of protein is precipitated by increasing amounts of antibody. You can check the antibody datasheet for recommended antibody concentration. As a guideline use: 1-5 l polyclonal antiserum 1 g affinity purified polyclonal antibody 0.2-1 l ascites fluid (monoclonal antibody) 20-100 l culture supernatant (monoclonal antibody) 2. Incubate the sample with the antibody for a fixed time between 1-12 hr (overnight) at 4C, preferably under gentle agitation or rotation. The length of the incubation period depends on the amount of protein and affinity properties of the antibody. 3. Meanwhile prepare the Sepharose beads. If using a monoclonal antibody choose protein G coupled Sepharose beads. If using a polyclonal antibody, protein A-coupled Sepharose beads are usually suitable (please refer to Choosing the protein beads table 9.1.5. below). If the beads come as a powder, incubate 100 mg of beads in 1 ml 0.1 M PBS, wash for 1 hr so they swell up, then centrifuge, remove the supernatant and discard. Add 1 ml PBS 0.1% BSA, mix for 1 hr and rinse in PBS 2 X. Remove the supernatant and add 400 l of buffer made with protease inhibitors (can be the same as the lysis buffer). The slurry is now ready for use. It can be stored at 4C for a few days; for longer periods keep the beads in PBS with 0.02% azide (rinse the beads extensively on the day of use and make up in fresh lysis buffer). You can also buy pre-swollen beads as slurry ready for use.
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It is advisable to use pipette tips with the end cut off to prevent damage to the beads. IgM antibody: Do not use protein-A or protein-G conjugated beads. Use Goat anti Mouse IgM ( or polyvalent Ig, or anti-heavy chain) beads.
4. Mix the slurry well and add 70-100 l of the beads to each sample. Always keep samples on ice. Beads will tend to stick to the sides of the tip so try to minimize the movement in the pipette and use a tip cut 5 mm from the top. 5. Incubate the lysate beads mixture at 4C under rotary agitation for 4 hr (the optimal incubation time can be determined in a preliminary experiment). 6. When the incubation period is over, centrifuge the tubes, remove the supernatant and wash the beads in lysis buffer 3 X (each time centrifuging at 4C and removing the supernatant).
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7. Finally, remove the last supernatant and add 25-50 l of 2 X loading buffer. Boil at 95-100C for 5 min to denature the protein and separate it from the protein-A/G beads, then centrifuge and keep the supernatant which contains the protein. You can then freeze the samples or run them on a SDS-PAGE gel.
Using loading buffer is the harshest elution method, and will also elute any non covalently bound antibodies and antibody fragments, which will appear on western blot gels. Antigens can be gently eluted with a glycine gradient (up to 1 M) to reduce the amount of eluted antibody. Please also see separate procedure for cross-linking antibody to Sepharose.
9.1.5. Choosing the correct beads- summary table

Species Immunoglobulin Isotype Human IgG1 Human IgG2 Human IgG3 Human IgG4 Human IgM Human IgE + +++ ++ + Use anti Mouse IgM + ++ +++ + ++ + +++ + +++ ++ ++ ++ +++ ++ ++ ++ +++ ++ ++ ++ Protein A +++ +++ +++ Use anti Human IgM + + +++ +++ ++ + Protein G +++ +++ +++ +++
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Human IgA Mouse IgG1 Mouse IgG2a Mouse IgG2b Mouse IgG3 Mouse IgM Rat IgG Rat IgG2a Rat IgG2b Rat IgG2c Chicken All isotypes Cow All isotypes Goat All isotypes Guinea Pig All isotypes Hamster All isotypes Horse All isotypes Pig All isotypes Rabbit All isotypes Sheep All isotypes
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References
Harlow, Ed, and David Lane. Using Antibodies. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, 1999. Bonifacino, Juan S. et al. Current Protocols in Immunology 8.3.1-8.3.28, New York: John Wiley, 2001.
9.2 Procedure for crosslinking the antibody to the beads:

Reducing the amount of antibody contamination in eluted protein solution: To enable elution of protein with little antibody contamination, for cleaner protein preparation and cleaner western blots, cross-linking the antibody to the beads is recommended. An example procedure for this is shown below (there is much information on this procedure on several websites). The target protein should then be eluted with a mild eluent, such as glycine buffer. More detailed buffer recipes can be found in the buffers section, page 77.
Reagents:
Cross linking reagent: Dimethyl pimelimidate (DMP) Stock concentration 13 mg/ml Elution reagent: 1 M glycine (Add conc. HCl to adjust to pH 3) Dilution buffer: PBS + 1 mg BSA per 1 ml PBS Wash buffer: 0.2 M triethanolamine in PBS (3.04 ml triethanolamine per 100 ml buffer) Quenching buffer: 50 mM ethanolamine in PBS (311.7 l per 100 ml) Preparation: 1. Wash beads 2 X in PBS. The end concentration should be 50% bead slurry. 2. Mix well with PBS and rotate overnight at 4C. Cross-linking: 1. Wash the beads by micro centrifuging (14,000 rpm for 1 min) into a pellet. Aspirate out the PBS supernatant. 2. Add dilution buffer at 1:1 ratio, mix gently and rotate for 10 min at 4C. Micro centrifuge and aspirate/discard the supernatant as before. 3. Prepare the antibody solution in Dilution buffer at the required concentration (see antibody datasheet for suggested concentration). Add diluted antibody at 1:1 ratio to the beads. Mix gently and rotate 1 hr at 4C. 3. Centrifuge and aspirate/discard the supernatant. 4. Add dilution buffer to beads at 1:1 ratio. Rotate for 5 min at 4C. Centrifuge and aspirate/discard the supernatant. 5. Add PBS to beads at 1:1 ratio. Centrifuge and aspirate/discard the supernatant. 6. Cross-linking: Dissolve 1 ml of prepared 13 mg/ml stock of DMP with 1 ml Wash buffer. Vortex immediately to mix. Add DMP solution to beads at 1:1 ratio. Rotate for 30 min at room temperature (RT).
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DMP is unstable in aqueous solution. Prepare solution immediately prior to use.
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Note: You will need to verify pH of DMP is between 8-9 before and after addition to beads (cross-linking efficiency is greatly reduced outside this pH range).
Wash the beads with wash buffer (rotate 5 min at RT, then spin and aspirate). Add DMP for second time at 1:1 ratio, rotate 30 min at RT, wash as before. Add DMP for third time at 1:1 ratio, rotate 30 min at RT, wash as before. 7. Quench and wash. Add Quench buffer at 1:1 ratio, rotate 5 min at RT, spin and aspirate; repeat. Wash with PBS. 8. Remove excess (unlinked) antibody: Wash with 1 M glycine pH 3. Rotate 10 min RT. Repeat. 9. Storage washes. Wash with buffer to be used for immunoprecipitation (usually PBS + Tween). Rotate 5 min RT. Wash three times and store in final wash (after rotation). Beads can be stored at 4C for a few days. Sodium azide 0.02 0.05% w/v can be added to prevent bacterial growth. Immunoprecipitation: The antibody bound beads can now be used in a normal IP procedure, as above. To prevent elution of antibody with the target protein, use a gentle glycine elution gradient (up to 1 M).
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9.3 Using IgM antibodies for immunoprecipitation

IgM antibodies are difficult to use in Immunoprecipitation due to its pentameric structure. IgM antibodies also do not bind well to protein A or protein G. There are two alternative methods available:
9.3.1. Protein L beads

Protein L is a 36 kDa immunoglobulin binding protein that can be purified from Peptostreptococcus magnus. Protein L binds antibodies through light chain interactions (whereas protein A and G bind the Fc heavy chain region of antibodies). Protein L binds a wider range of antibody classes than Protein A or G because no part of the heavy chain is involved in the binding interaction. It is able to bind all antibody classes, including IgG, IgM, IgA, IgE and IgD. Single chain variable fragments (ScFv) and Fab fragments also bind to Protein L. Binding of Protein L to immunoglobulins is restricted to those that contain kappa () light chains (i.e chain of the VL domain). In humans and mice, kappa () light chains predominate. The remaining immunoglobulins have lambda () light chains, which will not bind Protein L. Furthermore, Protein L is effective in binding only certain subtypes of kappa light chains. For example, it binds human VI, VIII and VIV subtypes but does not bind the VII subtype. Binding of mouse immunoglobulins is restricted to those having VI light chains. There are several advantages to using Protein L: 1. Protein L does not bind to bovine, sheep or goat antibodies, making it ideal for purification of mouse IgM from cell culture media containing bovine serum. 2. Protein L binds to kappa light chains on antibodies from a wide range of species without interfering with antigen binding sites, making it very suitable for immunoprecipitation using IgM antibodies. 3. It binds to all classes of Ig ( IgG, IgM, IgA, IgE and IgD) making it particularly useful for IgM purification which cannot be purified using protein A or G.
9.3.2. Use an IgG anti-IgM antibody on protein A or protein G beads.

This method involves coupling an IgG anti-IgM antibody to protein A or G beads (see method below). These beads can then be used in the normal immunopreciptiation procedure using the IgM antibody. The IgM will bind indirectly to the beads by binding to the anti-IgM antibody. The procedure below describes how to couple the anti-IgM antibody to protein A or G coated beads using dimethylpimelimidate (DMP): Reagents: 1. 200 mM Borate buffer + 3M NaCl pH 9.0 2. 20 mM Dimethylpimelimidate (DMP) in 200 mM borate buffer + 3 M NaCl, pH 9.0 3. 200 mM Ethanolamine pH8 (1:80 dilution of stock ethanolamine) 4. Phosphate buffered saline (PBS) 5. PBS + 0.1% sodium azide 6. 200 mM Glycine pH 2.5 7. Protein A or G beads (Sepharose)
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Method: We recommend using 2 mg of antibody per ml wet beads (use appropriate antibody/protein A or G combination). 1. Add 250 mg Protein A or G Sepharose beads (beads) to 2 ml PBS + 0.1% sodium azide, for 1 hr before use. This allows the beads to swell. 2. Mix the beads with an appropriate concentration of antibody for 2 hr at RT (using a rotator or roller). 3. Centrifuge at 2500 rpm for 5 min. 4. Wash the beads twice in 10 X volume of 200 mM borate buffer + 3 M NaCl. 5. Resuspend the beads in 20 mM DMP. 6. Rotate/agitate the beads for 30 min at RT. 7. Centrifuge the beads at 2,500 rpm for 5 min. 8. Wash the beads 2 X in 200 mM borate buffer + 3M NaCl. 9. Wash the beads 1 X in 20 mM ethanolamine. This stops the coupling reaction. 10. Resuspend the beads in 20 mM ethanolamine and rotate for 2 hr at RT. 11. Centrifuge the beads at 2,500 rpm for 5 min. 12. Wash the beads 2 X in PBS. 13. Wash the beads 2 X in 200 mM glycine.
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14. Wash the beads 2 X in PBS. 15. The beads can be stored at 4C in PBS + 0.1% sodium azide (Ratio of 1:1 PBS:beads). 16. These beads are now ready for use in immunoprecipitation with IgM antibody. From this point, proceed with the immunoprecipitation as described on our immunoprecipitation protocol, as on page 63.
9.4 Troubleshooting tips - IP High background

Carry over of proteins that are not detergent soluble Remove supernatant immediately after centrifugations. This should leave insoluble proteins in the pellet. If resuspension occurs, centrifuge again. Incomplete washing Wash well at relevant stages by placing a lid on the tube and inverting several times before centrifuging. Non specific proteins are binding to the beads. Beads are not pre-blocked enough with BSA. Make sure the BSA (fraction V) is fresh and incubate fresh beads 1 hr with 1% BSA in PBS. Wash 3-4 times in PBS before using them. Antibody used contains antibodies that are not specific enough. Use an affinity purified antibody, preferably pre-absorbed. Too much antibody used giving non specific binding Check the recommended amount of antibody suggested. Try using less antibody. Too many cells or too much protein in lysate, leading to a lot of additional (false positive) proteins in the eluate. Reduce the number of cells/lysate used. We recommend using 10-500 g cell lysate. Non specific binding of proteins to antibody If there are many proteins binding non specifically, then try reducing the amount of sample loaded onto the beads. You can also pre-clear the lysate by pre-incubating the prepared lysate with the beads before commencing with the immunoprecipitation (please see the protocol). This should clear the lysate of any proteins that are binding non specifically to the beads. Some researchers also use an irrelevant antibody of the same species of origin and same Ig subclass to pre-clear the lysate. Antigen degrading during immunoprecipitation Ensure fresh protease inhibitors are added when sample is lysed.
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High amount of antibody eluting

To much antibody eluting with the target protein Try reducing the amount of antibody. Cross-linking the antibody to the beads before the immunoprecipitation and eluting using a gentle glycine buffer gradient should significantly reduce the amount of antibody eluted.
No eluted target protein detected

Target protein not expressed in sample used or low level of target protein expression in sample used Check the expression profile of the target protein to ensure it will be expressed in the cells of your samples. If there is low level of target protein expression, increase the amount of lysate used. However, this may result in increased non specific binding so it would be advisable to pre-clear the lysate before commencing with the IP procedure. Insufficient antibody for capture of the target protein Check that the recommended amount of antibody is being used. The concentration of antibody may need to be increased for optimisation of results. Target protein has not eluted from the beads Ensure you are using the correct elution buffer and that it is at the correct strength and pH for elution of the protein. Antibody has not bound to immunoadsorbent beads Ensure you are using the correct beads for the antibody isotype used. Incorrect lysis buffer used. Check datasheet to see if the antibody detects denatured or native protein and ensure the correct lysis buffer is used.
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SECTION 10: ChIP

10.1 Cross-linking Chromatin Immunoprecipitation (X-ChIP) Protocol
Map proteins/histone modifications to genomic loci
Chromatin and associated proteins.
Cross-link
Start with 2 X 150 cm2 dishes of confluent cells (1 X 107 - 5 X 107 cells per dish) Add formaldehyde to a final conc of 0.75% Incubate 2 - 30 min RT Add glycine to a final conc of 125 mM Shake gently for 5 min
Cross-linking fixes proteins to DNA.
Cell collection
Wash cells with ice cold PBS Scrape and collect cells into 5 ml ice cold PBS and transfer to a new tube Wash dishes with 3 ml PBS to ensure all cells collected Centrifuge 5 min 1 000 g and remove supernatant Add FA lysis buffer to cell pellet (750 l per 1 X 107 cells) Sonicate to give a fragment size of 500 - 1000 bp Sonication generates sheared, soluble chromatin. Optimize by performing a time course and purify DNA. Analyse fragment size on 1.5 % agarose gel.
Cell lysis Sonication
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Centrifuge 30 sec 4C 8 000 g to pellet cell debris Transfer supernatant containing chromatin to a new tube Remove 50 l (INPUT) and purify DNA to calculate the DNA concentration Use an amount of chromatin equivalent to approximately 25 g of DNA per IP Dilute 1:10 with RIPA buffer Add 1 - 10 g of antibody Antibody binds to target and associated DNA is isolated. DNA fragments not associated are removed during washes.
Immunoprecipitation
(Continued Overleaf)
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Add 20 l of protein A/G beads Rotate overnight 4C Centrifuge 1 min 2 000 g Wash 3 X with wash buffer Wash 1 X with final wash buffer.
Elute protein / DNA complex
Add 120 l of Elution Buffer to the protein A/G beads Rotate 15 min 30C Centrifuge 1 min 2 000 g Transfer supernatant containing protein/DNA complex to a new tube
Reverse cross-links and purify DNA EITHER

PCR purification kit Phenol:chloroform extraction
Add 2 l RNase A (0.5 mg/ml) Heat 65C 4 - 5 hr
Add 5 l proteinase K (20 mg/ml) Heat 65C 4 - 5 hr Extract DNA using phenol:chloroform Precipitate with ethanol and 10 l glycogen (5 mg/ml) Resuspend pellet in 100 l H2O
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Purify DNA using PCR purification kit according to manufacturer's instructions
DNA Analysis
Analyze DNA isolated by: quantitative PCR, sequencing (ChIP-seq), microarray (ChIP-chip).
ChIP is a powerful tool that specifically correlates the localization of proteins or their modifications to regions of the genome. Chromatin is isolated and antibodies to the antigen of interest are used to determine whether the target binds to a specific DNA sequence. ChIP can also be used to map the distribution of the target across the genome in a spatial and/or temporal manner (using a microarray or DNA sequencing). This protocol provides specific details of how a cross-linking ChIP (X-ChIP) experiment can be performed.
1. Cross-linking and Cell Harvesting
Formaldehyde is used to cross-link the proteins to the DNA. Cross-linking is a time dependent procedure and optimization will be required. We would suggest cross-linking the samples for 2-30 min. Excessive cross-linking reduces antigen accessibility and sonication efficiency. Epitopes may also be masked. Glycine is added to quench the formaldehyde and terminate the cross-linking reaction.
1.1. Start with 2 confluent 150 cm2 dishes (1x107- 5x107 cells per dish). Cross-link proteins to DNA by adding formaldehyde drop wise directly to the media to a final concentration of 0.75 % v/v and rotate gently at room temperature (RT) for 10 min. 1.2. Add glycine to a final concentration of 125 mM to the media and incubate with shaking for 5 min at RT.
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1.3. Rinse cells 2 X with 10 ml cold PBS. 1.4. Scrape cells into 5 ml cold PBS and transfer into 50 ml tube. 1.5. Add 3 ml PBS to dishes and transfer the remainder of the cells to the 50 ml tube. 1.6. Centrifuge for 5 min, 1,000 g. 1.7. Carefully aspirate off supernatant and resuspend pellet in FA Lysis Buffer (750 l per 1x107 cells).
When using suspension cells, start with 1x107- 5x107 cells and treat with both 0.75 % v/v formaldehyde and glycine as described above (Section 1). Pellet cells by centrifugation (5 min, 1000 g). Wash 3 X with cold PBS and resuspend pellet in FA Lysis Buffer (750 l per 1x107 cells). Proceed to Step 2.1.
2. Sonication
When using tissue as a starting material (see Section 10.2), generate a unicellular suspension and start the protocol here at the sonication stage.
2.1. Sonicate lysate to shear DNA to an average fragment size of 500-1000 bp. This will need optimizing as different cell lines require different sonication times.
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The cross-linked lysate should be sonicated over a time course to identify optimal conditions. Samples should be removed over the time course and DNA isolated as described in Section 3. The fragment size should be analyzed on a 1.5 % w/v agarose gel as demonstrated in Figure 1.
2.2. After sonication, pellet cell debris by centrifugation for 30 sec, 4C, 8,000 g. Transfer supernatant to a new tube. This chromatin preparation will be used for the immunoprecipitation (IP) in Step 4. 2.3. Remove 50 l of each sonicated sample. This sample is the INPUT and is used to quantify the DNA concentration (see Step 3) and as a control in the PCR step.
The sonicated chromatin can be snap frozen in liquid nitrogen and stored at -80C for up to 2 months. Avoid multiple freeze thawing.
Figure 1. U2OS cells were sonicated for 5, 10, 15 and 20 min. The fragment size decreases during the time course. The optimal fragment size is observed 15 min after sonication. NOTE; sonicating for too long will disrupt nucleosome-DNA interactions so the band size should not be smaller than 200bp.
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3. Determination of DNA concentration

3.1. The INPUT samples are used to calculate the DNA concentration for subsequent IPs. Purify the DNA using either a PCR purification kit (add 70 l of Elution Buffer and proceed to Step 3.2a) or phenol:chloroform (add 350 l of Elution Buffer and proceed to Step 3.2b). 3.2a. Add 2 l RNase A (0.5 mg/ml). Heat with shaking at 65C for 4-5 hr (or overnight) to reverse the cross-links. Purify the DNA using a PCR purification kit according to the manufacturers instructions. The samples can be frozen and stored at -20C.
Samples are treated with RNase A as high levels of RNA will interfere with DNA purification when using the PCR purification kit. Yields can be severely reduced as the columns become saturated.
3.2b. Add 5 l proteinase K (20 mg/ml). Heat with shaking at 65C for 4-5 hr (or overnight) to reverse the cross-links. Extract the DNA with phenol:chloroform followed by ethanol precipitation in the presence of 10 l glycogen (5 mg/ml). Resuspend in 100 l H2O. The samples can be frozen and stored at -20 C.
Samples are treated with proteinase K, which cleaves peptide bonds adjacent to the carboxylic group of aliphatic and aromatic amino acids. Cross-links between proteins and DNA are disrupted to aid DNA purification.
3.3. To determine the DNA concentration, transfer 5 l of the purified DNA into a tube containing 995 l TE to give a 200 fold dilution and measure the OD260. Calculate the DNA concentration of the chromatin preparation in g/ml. Concentration of DNA in g/ml = OD260 x 10,000.
4. Immunoprecipitation SECTION 10
4.1. Use the chromatin preparation from Step 2.2. Chromatin containing approximately 25 g of DNA per IP is recommended. Dilute each sample 1:10 with RIPA Buffer. You will need one sample for the specific antibody and one sample for the control (beads only). 4.2. Add primary antibody to all samples except the control. The amount of antibody to be added should be determined empirically. 1-10 g of antibody per 25 g of DNA often works well. 4.3. Add 20 l of protein A/G beads (pre-adsorbed with sonicated single stranded herring sperm DNA and BSA, see step 4.3a) to all samples and IP overnight with rotation at 4C. 4.3a Preparation of protein A/G beads with single-stranded herring sperm DNA: if using both Protein A and Protein G beads, mix an equal volume of Protein A and Protein G beads and wash 3 X in RIPA Buffer. Aspirate RIPA Buffer and add single stranded herring sperm DNA to a final concentration of 75 ng/l beads and BSA to a final concentration of 0.1 g/l beads. Add RIPA Buffer to twice the bead volume and incubate for 30 min with rotation at RT. Wash once with RIPA Buffer and add RIPA Buffer to twice the bead volume.
Protein A beads, protein G beads or a mix of both should be used. The table in section 9 page 66 shows the affinity of protein A and G beads to different immunoglobulin isotypes.
4.4. Centrifuge the protein A/G beads for 1 min, 2,000 g and remove the supernatant. 4.5. Wash beads 3 X with 1 ml wash buffer. Centrifuge 1 min, 2,000 g. 4.6. Wash beads 1 X with 1 ml Final wash buffer. Centrifuge 1 min, 2,000 g.
If high background is observed, additional washes may be needed. Alternatively, the sonicated chromatin may also be pre-cleared by incubating with the Protein A/G beads for 1 hr prior to Step 4.2. Any non specific binding to the beads will be removed during this additional step. Transfer the supernatant (sonicated chromatin) to a new tube and incubate with the antibody and beads as described in Step 4.2 onwards.
5. Elution and reverse cross-links

5.1. Elute DNA by adding 120 l of elution buffer to the protein A/G beads and rotate for 15 min, 30 C. 5.2. Centrifuge for 1 min 2,000 g, and transfer the supernatant into a fresh tube. The samples can be stored at -20 C
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5.3. The DNA can be purified using a PCR purification kit (proceed with Step 3.2a) or phenol:chloroform (add 280 l of Elution Buffer and proceed with Step 3.2b). 5.4. DNA levels are quantitatively measured by real time PCR. Primers and probes are often designed using software provided with the real time PCR apparatus. Alternatively, online design tools may be used.
6. Chromatin preparation from tissues for ChIP

This protocol describes how chromatin is prepared from tissue, which can subsequently be used for ChIP. It is recommended that 30 mg of liver tissue is used for each ChIP/antibody. However, this amount may vary for other tissues. The exact amount of tissue depends upon protein abundance, antibody affinity and the efficiency of cross-linking. The protocol was optimized using 5-15 g chromatin for each ChIP assay. The exact chromatin concentration should be determined for each tissue type before starting the cross-link ChIP (X-ChIP) assay. Our X-ChIP protocol should be used after the chromatin preparation detailed below. Protease inhibitors should be included in all solutions used, including PBS [PMSF (10 l/ml), aprotinin (1 l/ml) and leupeptin (1 l/ml)]. This section was adapted from protocols kindly provided by Henriette OGeen, Luis G. Acevedo and Peggy J. Farnham. 6.1. Cross-linking
Frozen tissues should be thawed on ice. (This process could take hours depending on the amount of tissue). It is important that the frozen tissue samples do not reach high temperatures, in order to prevent sample degradation by proteases. Samples should be kept on ice at all times and all steps performed quickly to minimize thawing. Tissue should be cut in a petri dish resting on a block of dry ice.
6.1.1. Chop frozen or fresh tissue into small pieces using 2 razor blades (between 1-3 mm3). 6.1.2. Determine the weight of an empty 15 ml conical tube, transfer tissue into the tube and weigh again to calculate the amount of tissue. 6.1.3. Prepare cross-linking solution in fume hood. Use 10 ml PBS per gram of tissue. Add formaldehyde to a final concentration of 1.5 % v/v and rotate tube at RT for 15 min. 6.1.4. Stop the cross-linking reaction by adding glycine to a final concentration of 0.125 M. Continue to rotate at RT for 5 min. 6.1.5. Centrifuge tissue samples for 5 min, 720 rpm, 40C. 6.1.6. Aspirate media and wash with 10 ml ice cold PBS. Centrifuge for 5 min, 720 rpm, 4C and discard wash buffer.
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The tissue may be snap frozen at this stage in liquid nitrogen and stored at -80C. Avoid multiple freeze thaws. If using immediately, resuspend tissue in 10 ml cold PBS per gram of starting material. Place on ice.
6.2. Tissue disaggregation The Medimachine from Becton Dickinson may be used to obtain a single cell suspension. Use 2 medicones (50 m) per gram of tissue to process. 6.2.1. Cut the end off a 1 ml pipette tip to make the orifice larger. 6.2.2. Add between 50-100 mg (3-4 chunks) of tissue resuspended in 1 ml of PBS. 6.2.3. Add this solution to the medicone and grind tissue for 2 min. 6.2.4. Collect cells from the medicone by inserting an 18 gauge blunt needle attached to a 1 ml syringe. Transfer cells to a conical tube on ice. 6.2.5. Repeat step 2.2 until all the tissue is processed. 6.2.6. Check the cell suspension using a microscope to ensure a unicellular suspension has been obtained. If more grinding is necessary, add more PBS to the tissue and repeat steps 2.2 to 2.5 until all tissue is ground into a homogeneous suspension. 6.2.7. Centrifuge cells for 10 min, 1000 rpm, 4C. Measure/estimate cell pellet volume for next step. 6.2.8. Carefully aspirate off supernatant and resuspend pellet in FA Lysis Buffer (750 l per 1x107 cells). 6.2.9. Continue with the X-ChIP protocol from stage 2 (sonication).
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10.2 Troubleshooting tips - ChIP High background in non specific antibody controls
Non specific binding to Protein A or G beads Include a pre-clearing step, whereby the lysed sample is mixed with beads alone for 1 hr and removed prior to adding the antibody. The ChIP buffers may be contaminated Prepare fresh lysis and wash solutions. Some Protein A or G beads give high background Some Protein A or G beads can give high background levels. Find a suitable supplier that provides the cleanest results with low background in the non specific control.
Low resolution with high background across large regions

DNA fragment size may be too large DNA fragmentation should be optimised when using different cell types. Both sonication times and enzyme incubation times may be varied. We would suggest a DNA fragment size of no larger than 1.5 kbp. If chromatin is being digested using enzymes, mononucleosomes (175 bp) can be obtained.
Low signal
The chromatin size may be too small Do not sonicate chromatin to a fragment size of less than 500 bp. Sonication to a smaller size can displace nucleosomes as intra nucleosomal DNA becomes digested. If performing N-ChIP, enzymatic digestion is generally sufficient to fragment chromatin. If performing X-ChIP, the cells may have been cross-linked for too long Cross-link with formaldehyde for 10-15 min and wash well with PBS. Cells may need to be treated with glycine to quench the formaldehyde. Excessive cross-linking can reduce the availability of epitopes and thus decrease antibody binding.
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Insufficient starting material We would suggest using 25 g of chromatin per immunoprecipitation. Insufficient antibody included in the immunoprecipitation We would suggest using between 3-5 g of antibody in the first instance. This could be increased to 10 g if no signal is observed. Specific antibody binding is being eliminated Do not use NaCl concentrations higher than 500 mM in the wash buffers as this may be too stringent and remove specific antibody binding. Cells are not effectively lysed We would suggest using RIPA buffer to lyse cells No antibody enrichment at region of interest The epitope is not found at the region of interest. Be sure to include a positive control antibody to confirm the procedure is working well e.g., a H3K4me3 antibody at active promoters or a H3K9me3 antibody at heterochromatic loci. Some monoclonal antibodies may not be suitable for X-ChIP The epitope recognized by the monoclonal antibody may have become masked during cross-linking, thus preventing epitope recognition. We would suggest using polyclonal antibodies that will recognize multiple epitopes as there is an increased chance of immunoprecipitating the protein of interest. The wrong antibody affinity beads were used Protein A and G are bacterial proteins that bind various classes of immunoglobulins with varying affinities. Use an affinity matrix that will bind your antibody of interest. We would suggest using a mix of Protein A and protein G that have been coupled to sepharose.
Problems with PCR amplification on immunoprecipitated DNA

High signal in all samples after PCR, including no template control Contamination in real time PCR solutions. We suggest preparing new solutions from stocks No DNA amplification in samples Be sure to include standard/input DNA to confirm that the primers are working well.
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SECTION 11: Buffers

11.1 Standard PBS, TBS, TBS Tween
PBS (10x) 80 g of NaCl 2.0 g of KCl 14.4 g of Na2HPO4 2.4 g of KH2PO4 Mix in 800 ml ultra pure water and adjust pH to 7.4 with pure HCl. Top up with ultra pure water to 1 L. TBS (10x) 24.23 g Trizma HCl 80.06 g NaCl Mix in 800 ml ultra pure water and adjust pH to 7.6 with pure HCl. Top up with ultra pure water to 1 L. TBST (0.1% Tween20) For 1 L: 100 ml of TBS 10x + 890 ml ultra pure water + 10ml Tween 20 (10%) Tween 20 is very viscous and will stick to the tip of measuring pipettes. Be sure to add the right amount of detergent to the Tris buffer. We recommend a 10% solution as is easier to dispense than undiluted Tween 20.
11.2 Western blot

Lysis buffers: These buffers may be stored at 4C for several weeks or for up to a year aliquotted and stored at -20C. Nonidet-P40 (NP40) buffer 150 mM NaCl 1.0% NP-40 (possible to substitute with 0.1% Triton X-100) 50 mM Tris-HCl pH 8.0 Protease Inhibitors RIPA buffer (Radio Immuno Precipitation Assay buffer) 150 mM NaCl 1.0% NP-40 or 0.1% Triton X-100 0.5% sodium deoxycholate 0.1% SDS (sodium dodecyl sulphate) 50 mM Tris-HCl pH 8.0 Protease Inhibitors More denaturing than NP-40 or Triton X-100 lysis buffer, RIPA buffer contains the ionic detergents SDS and sodium deoxycholate as active constituents and is particularly useful for nuclear membrane disruption for nuclear extracts. RIPA buffer gives low background but can denature kinases.
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The 10% sodium deoxycholate stock solution (5 g into 50 ml) must be protected from light.
Tris-HCl buffer 20 mM Tris-HCl pH 7.5 Protease Inhibitors Tris-Triton buffer (Cytoskeletal proteins): 10 mM Tris, pH 7.4 100 mM NaCl 1 mM EDTA 1 mM EGTA 1% Triton X-100 10% glycerol 0.1% SDS 0.5% sodium deoxycholate Protease Inhibitors
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The 10% sodium deoxycholate stock solution (5 g into 50 ml) must be protected from light.
Non-denaturing lysis buffer 20 mM Tris HCl pH 8 137 mM NaCl 10% glycerol 1% NP-40/Triton X-100 2 mM EDTA Protease Inhibitors Use for antigens that are detergent soluble and can be recognised in native form by the antibody. Triton X-100 can be substituted for NP-40. Detergent-free soluble protein lysis buffer 5 mM EDTA 0.02% Sodium Azide In PBS Protease Inhibitors Some soluble proteins may not require use of detergents. Use this buffer with mechanical breakage of cells, e.g. repeated passage through a syringe or homogenization with a Dounce homogenizer. Denaturing lysis buffer/buffer for non-detergent soluble antigens: 1% SDS 5 mM EDTA Immediately before use add: 10 mM dithiothreitol or beta-mercaptoethanol Protease inhibitors 15 U/ml DNase1 Epitopes of native proteins are not accessible to antibodies that only recognise denatured proteins. When harvesting and lysing the cells, heat the cells in denaturing lysis buffer. This method can also be used for antigens that cannot be extracted from the cell with non-ionic detergents. Use of DNase1 will aid extraction of proteins from chromatin. Running and blotting buffers Laemmli 2X buffer / loading buffer4% SDS 10% 2-mercaptoethanol 20% glycerol 0.004% bromophenol blue 0.125 M Tris-HCl Check the pH and adjust pH to 6.8. Running buffer 25 mM Tris base 190 mM glycine 0.1% SDS Check the pH, which should be about pH 8.3. Adjust if necessary. Transfer buffer (Wet) 25 mM Tris base 190 mM glycine 20% methanol The pH should be about pH 8.3. Adjust if necessary. For proteins larger than 80 kDa, we recommend that SDS is included at a final concentration of 0.1%.
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Transfer buffer (semi-dry) 48 mM Tris 39 mM glycine 20% methanol 0.04% SDS Blocking buffer: 5% milk or BSA (bovine serum albumin) Add to TBST buffer. Mix well and filter. Failure to filter can lead to spotting where tiny dark grains will contaminate the blot during colour development.
11.3 Immunohistochemistry/Immunocytochemistry (IHC)

Fixation buffers Formalin Solution (10%, buffered neutral): 3.7-4% Formaldehyde (37-40%) 33 mM NaH2PO4 46 mM Na2HPO4 (anhydrous) Paraformaldehyde (4%, buffered neutral): 8% Paraformaldehyde 0.2 M Phosphate Buffer (PB), pH 7.4: 53 mM NaH2PO4 154 mM Na2HPO4 Heat 8% PFA solution at 60C while stirring (do not allow the solution to go above 60C). Once the solution has reached 60C and the PFA is dissolved, add 500 ml of 0.2 M phosphate buffer, to bring the solution to 4% PFA in 0.1 M phosphate. Carefully add 1 N NaOH dropwise until solution is clear (try 1-2 drops per 500 ml; if still not clear, add a few more drops. Alternatively, you can add 2 pellets of solid NaOH in 1-2 L of solution). Cool the solution and filter. The solution should be at pH 7.4. Do not adjust the pH using acid or base! If you need to adjust the pH, make up a separate 0.2 M solution of either the monobasic or dibasic sodium phosphate (depending on how you need to adjust the pH) and add accordingly.
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PFA should always be made up fresh on the same day you wish to use it. Storage overnight at 4C is possible, but it will not fix as well the second day. It is possible possible to freeze the PFA solution at -20C, but for consistency of results, tissue should either be fixed always with fresh PFA or always with freshly thawed PFA.
Bouin Solution (especially for preserving soft and delicate structures such as brain tissues) 75 ml picric acid (saturated) 25 ml formaldehyde (37-40%) 5 ml glacial acetic acid Mix well. Antigen retrieval buffers: Sodium Citrate Buffer pH 6.0 10 mM Sodium citrate (Tri-sodium citrate (dihydrate)) 0.05% Tween 20 Mix to dissolve sodium citrate and adjust pH to 6.0 with 1N HCl. Add Tween 20 and mix well. Store at room temperature for 3 months or at 4C for longer storage. Tris-EDTA Buffer pH9.0 10 mM Tris Base 1 mM EDTA 0.05% Tween 20 Mix to dissolve and adjust pH to pH 9.0. Add Tween 20 and mix well. Store at room temperature for 3 months or at 4C for longer storage. Enzymatic antigen retrieval buffers: Trypsin Stock Solution 0.5% Trypsin Mix to dissolve in distilled water. Store at -20C.
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Calcium Chloride Stock Solution (1%) 1% Calcium chloride Mix well in distilled water. Store at 4C. Trypsin Working Solution 0.05% Trypsin (Use 0.5% Trypsin stock solution 0.1% Calcium chloride (Use 1% Calcium chloride stock solution) 8 ml Distilled Water Mix well in distilled water and adjust pH to 7.8 with 1 M NaOH Store at 4C for one month or -20C for long term storage.
11.4 ELISA
Bicarbonate/carbonate coating buffer (100 mM) pH9.6 Antigen or antibody should be diluted in coating buffer to immobilize them to the wells: 29 mM Na2CO3, 71 mM NaHCO3 Blocking solution: Commonly used blocking agents are 1% BSA , serum, non-fat dry milk, casein, gelatin in PBS. Wash solution: Usually PBS or Tris -buffered saline (pH 7.4) with detergent such as 0.05% (v/v) Tween 20 (TBST). Antibody dilution buffer: Primary and secondary antibody should be diluted in 1x blocking solution to reduce Non-specific binding.
11.5 Flow cytometry SECTION 11

FACS buffer / antibody dilution buffer 10% FCS 1% sodium azide In PBS Permeabilization 0.1-1% Triton X-100 / NP-40 In PBS. Tween 20, Saponin, Digitonin and Leucoperm may also be used and are mild membrane solubilisers. Use at 0.5% in PBS Fixative 0.01%-0.1% paraformaldehyde In PBS
11.6 Immuno Precipitation

See western blot buffers RIPA (RadioImmunoPrecipitation Assay) buffer See western blot buffers
11.7 ChIP
FA Lysis buffer 50 mM HEPES-KOH pH 7.5 140 mM NaCl 1 mM EDTA pH 8 1% Triton X-100 0.1% Sodium Deoxycholate 0.1% SDS Protease Inhibitors RIPA buffer 50 mM Tris-HCl pH 8 150 mM NaCl 2 mM EDTA pH 8 1% NP-40 0.5% Sodium Deoxycholate 0.1% SDS Protease Inhibitors
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Wash buffer 0.1% SDS 1% Triton X-100 2 mM EDTA pH 8 150 mM NaCl 20 mM Tris-HCl pH 8 Final wash buffer 0.1% SDS 1% Triton X-100 2 mM EDTA pH 8 500 mM NaCl 20 mM Tris-HCl pH 8 Elution buffer 1% SDS 100 mM NaHCO3 Proteinase K Dissolve in H2O at 20 mg/ml, store at -20C.
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SECTION 12: Antibody storage guide

Guidelines for the storage of different types of antibody, avoiding contamination or damage
Please always check datasheets for specific storage recommendations. Abcam can not guarantee the performance of antibodies that have not been stored correctly. With proper storage and handling, most antibodies should retain activity for months, if not years.
Storage temperatures and conditions For many of our antibodies, freezing at -20C or -80C in small aliquots is the optimal storage condition. Aliquotting minimizes damage due to freezing and thawing, as well as contamination introduced by pipetting from a single vial multiple times. Aliquots are to be frozen and thawed once, with any remainder kept at 4C. Upon receiving the antibody, centrifuge at 10,000 x g for 20 sec to pull down solution that is trapped in the threads of the vial, and transfer aliquots into low-protein-binding microcentrifuge tubes. The size of the aliquots will depend on how much one typically uses in an experiment. Aliquots should be no smaller than 10 l; the smaller the aliquot, the more the stock concentration is affected by evaporation and adsorption of the antibody onto the surface of the storage vial. In most cases, with the possible exception of ascites fluids which may contain proteases and should be frozen as soon as possible, storage at 4C upon receipt of the antibody is acceptable for one to two weeks, followed by freezing for long-term storage. Again, it is important to follow the recommendations on the datasheet. Exceptions and other special conditions: Enzyme-conjugated antibodies, should not be frozen at all and should instead be kept at 4C. Freezing and thawing will reduce enzymatic activity in addition to affecting the antibody binding capacity. Conjugated antibodies, whether conjugated to fluorochromes, enzymes, or biotin, should be stored in dark vials or wrapped in foil. Exposure to light will compromise the activity of conjugates. Fluorescent conjugates in particular are susceptible to photo-bleaching and should be protected from light during all phases of an experiment. IgG3 isotype antibodies are unique in their tendency to form aggregates upon thawing and should always be stored at 4C. Preventing contamination with sodium azide To prevent microbial contamination, sodium azide can be added to an antibody preparation to a final concentration of 0.02% (w/v). Many Abcam antibodies already contain this preservative at concentrations ranging from 0.02 to 0.05%. This will be indicated on the datasheets in the section titled Storage buffer. When NOT to use sodium azide: If staining or treating live cells with antibodies, or if using antibodies for in vivo studies, be sure to use preparations that do not contain sodium azide.This antimicrobial agent is toxic to most other organisms as well: it blocks the cytochrome electron transport system. Sodium azide will interfere with any conjugation that involves an amine group, and should be removed before proceeding with the conjugation. After conjugation, antibodies can be stored in sodium azide but 0.01% thimerosal (merthiolate), which does not have a primary amine, is an acceptable alternative. Sodium azide can be removed from antibody solutions by dialysis or gel filtration. The molecular weight of IgG is 150,000 daltons (IgM is ~ 600,000); the molecular weight of sodium azide is 65 daltons. A micro-dialysis unit with a cut off at 14,000 daltons will retain the antibody as the azide diffuses out. In a beaker on a magnetic stirrer kept at 4C, use at least a liter of cold PBS per ml of antibody and stir the dialysis unit for 6 hr. Change the PBS twice, stirring at least 6 hr for each change. If possible, all materials should be sterilized and the resulting preparation should be handled aseptically. Freeze/thaw damage Repeated freeze/thaw cycles can denature an antibody, causing it to form aggregates that reduce the antibodys binding capacity. Storing at -20C should be adequate for most antibodies; there is no appreciable advantage to storing at -80C. The freezer must not be of the frost-free variety. These cycle between freezing and thawing (to reduce frost-build-up), which is exactly what should be avoided. For the same reason, antibody vials should be placed in an area of the freezer that has minimal temperature fluctuations, for instance towards the back rather than on a door shelf. Some researchers add the cryoprotectant glycerol to a final concentration of 50% to prevent freeze/thaw damage; glycerol will lower the freezing point to below -20C. While this may be acceptable for many antibodies, only a small percentage of the antibodies we offer have been tested for stability in this storage condition and our guarantee only applies to antibodies stored as recommended on the datasheet. Storing solutions containing glycerol at -80C is not advised since this is below the freezing point of glycerol. Please be aware that glycerol can be contaminated with bacteria. If adding glycerol or any cryoprotectant, care should be taken to obtain a sterile preparation. Diluting antibodies to working concentration and storing at 4C for more than a day should be avoided. Proteins in general are less susceptible to degradation when stored at higher concentrations, ideally 1 mg/ml or higher. This is the rationale for including proteins such as BSA to the antibody solution as stabilizers. The added protein also serves to minimize loss of antibody due to binding to the vessel wall. For antibodies that one intends to conjugate, stabilizing proteins should not be added since they will compete with the antibody and reduce the efficiency of the conjugation.
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Abcam Protocols Book 2010

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Abcam Protocols Book 2010

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Protocols book

Ordering and contact details

See all our protocols online at: www.abcam.com/protocols

Worldwide reach, next day delivery

Benefits of an Abcam Account

Promotion Submit an Abreview

Submit an image with your Abreview

See all our protocols online at: www.abcam.com/protocols

SECTION 1: Antibodies and antibody structure

Fab and Fc regions

IgE IgG1 IgG2a IgG2b IgG3 IgG4

SECTION 2: Antibody purification

Tissue culture supernatant

Protein A/G purification

Antibody purification at Abcam:

SECTION 3: Choosing an antibody and antibody dilution

Unpurified antibody suggested dilutions and concentrations:

Ascites 1/1000 1/100 1/10000 1/1000 1/100 5 to 10 mg/ml

Purified Antibody 1 g/ml 5 g/ml 0.1 g/ml 1 g/ml 1 to 10 g/ml

See all our protocols online at: www.abcam.com/protocols

Excitation and emission spectral profiles:

Laser line (633) Excitation Emission Cy5

Laser line (488) Excitation Emission PE-Cy5

Energy level diagram - single dye:

Es Excitation 2 3 Fluorescence (Emission)

Energy level diagram - tandem dye:

4 Energy transfer Laser 1 Excitation 2 D A 5 Emission

Es D Excitation 2 3 4 A 5 Fluorescence (Emission)

4.2 Fluorochrome table:

Nucleic acid probes:

See all our protocols online at: www.abcam.com/protocols

SECTION 5: Western blotting

Loading the gel

Prepare running buffer Assemble the gel in the tank

Running the gel

Western blot (continued)

Blocking Primary antibody incubation

Band of protein / antigen on membrane

Secondary antibody incubation

Conjugated Secondary antibody

Scan and analyze results

5.1. Sample preparation

5.3. Transfer of proteins and staining (western blotting)

5.4. References 5.5. Troubleshooting tips

5.1. Sample preparation

See all our protocols online at: www.abcam.com/protocols

Aprotinin Leupeptin Pepstatin A PMSF EDTA EGTA Na Fluoride

The buffer (with inhibitors) should be ice-cold prior to homogenization.

Migration buffer With SDS No SDS With SDS No SDS

Running the gel

Protein size (kDa) 4-40 12-45 10-70 15-100 25-200

Gel percentage (%) 20 15 12.5 10 8

GAPDH Tubulin VDCA1/Porin COXIV Lamin B1 TATA binding protein TBP

5.3. Transfer of proteins and staining

Note on transfer of large and small proteins

5.5. Troubleshooting tips western blotting

High background SECTION 5

Uneven white spotson the blot

Black dots on the blot

White bands on a black blot (negative of expected blot)

MW marker lane is black

The band of interest is very low/high on the blot

Smile effect of the bands